1
|
Rocha AL, Pai V, Perkins G, Chang T, Ma J, Chu Q, Vaughan JM, Diedrich JK, Ellisman MH, Saghatelian A. An inner mitochondrial membrane microprotein from the SLC35A4 upstream ORF regulates cellular metabolism. J Mol Biol 2024:168559. [PMID: 38580077 DOI: 10.1016/j.jmb.2024.168559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Revised: 03/29/2024] [Accepted: 03/31/2024] [Indexed: 04/07/2024]
Abstract
Upstream open reading frames (uORFs) are cis-acting elements that can dynamically regulate the translation of downstream ORFs by suppressing downstream translation under basal conditions and, in some cases, increasing translation under stress conditions. Computational and empirical methods have identified uORFs in the 5'-UTRs of approximately half of all mouse and human transcripts, making uORFs one the largest regulatory elements known. Because the prevailing dogma was that eukaryotic mRNAs produce a single functional protein, the peptides and small proteins, or microproteins, encoded by uORFs are under studied. We hypothesized that a uORF in the SLC35A4 mRNA is producing a functionalmicroprotein (SLC35A4-MP) because of its conserved amino acid sequence. Through a series of biochemical and cellular experiments, we find that the 103-amino acid SLC35A4-MP is a single-pass transmembrane inner mitochondrial membrane (IMM) microprotein. The IMM contains the protein machinery crucial for cellular respiration and ATP generation, and loss of function studies with SLC35A4-MP significantly diminish maximal cellular respiration, indicating a vital role for this microprotein in cellular metabolism. The findings add to the growing list of functional microproteins and, more generally, indicate that uORFs that encode conserved microproteins are an untapped reservoir of functional microproteins.
Collapse
Affiliation(s)
- Andrea L Rocha
- Clayton Foundation Laboratories for Peptide Biology, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Victor Pai
- Clayton Foundation Laboratories for Peptide Biology, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Guy Perkins
- National Center for Microscopy and Imaging Research, Center for Research in Biological Systems, Department of Neurosciences, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Tina Chang
- Clayton Foundation Laboratories for Peptide Biology, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Jiao Ma
- Clayton Foundation Laboratories for Peptide Biology, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Qian Chu
- Clayton Foundation Laboratories for Peptide Biology, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Joan M Vaughan
- Clayton Foundation Laboratories for Peptide Biology, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Jolene K Diedrich
- Mass Spectrometry Core for Proteomics and Metabolomics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA, USA
| | - Mark H Ellisman
- National Center for Microscopy and Imaging Research, Center for Research in Biological Systems, Department of Neurosciences, School of Medicine, University of California San Diego, La Jolla, CA, USA.
| | - Alan Saghatelian
- Clayton Foundation Laboratories for Peptide Biology, Salk Institute for Biological Studies, La Jolla, CA, USA.
| |
Collapse
|
2
|
Noguchi GM, Castillo VC, Donaldson CJ, Flisher MR, Momen AT, Saghatelian A, Huising MO. Urocortin3 contributes to paracrine inhibition of islet alpha cells in mice. J Endocrinol 2024:JOE-24-0018. [PMID: 38593829 DOI: 10.1530/joe-24-0018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 04/08/2024] [Indexed: 04/11/2024]
Abstract
Pancreatic alpha cell activity and glucagon secretion lowers as glucose levels increase. While part of the decrease is regulated by glucose itself, paracrine signaling by their neighboring beta and delta cells also plays an important role. Somatostatin from delta cells is an important local inhibitor of alpha cells at high glucose. Additionally, Urocortin3 (UCN3) is a hormone that is co-released from beta cells with insulin and acts locally to potentiate somatostatin secretion from delta cells. UCN3 thus inhibits insulin secretion via a negative feedback loop with delta cells, but its role with respect to alpha cells and glucagon secretion is not understood. We hypothesize that the somatostatin-driven glucagon inhibition at high glucose is regulated in part by UCN3 from beta cells. Here, we use a combination of live functional Ca2+ and cAMP imaging as well as direct glucagon secretion measurement, all from alpha cells in intact mouse islets, to determine the contributions of UCN3 to alpha cell behavior. Exogenous UCN3 treatment decreased alpha cell Ca2+ and cAMP levels and inhibited glucagon release. Blocking endogenous UCN3 signaling increased alpha cell Ca2+ by 26.8 ± 7.6%, but this did not result in increased glucagon release at high glucose. Furthermore, constitutive deletion of Ucn3 did not increase Ca2+ activity or glucagon secretion relative to controls. UCN3 is thus capable of inhibiting mouse alpha cells, but, given the subtle effects of endogenous UCN3 signaling on alpha cells, we propose that UCN3-driven somatostatin may serve to regulate local paracrine glucagon levels in the islet instead of inhibiting gross systemic glucagon release.
Collapse
Affiliation(s)
- Glyn M Noguchi
- G Noguchi, Department of Neurobiology, Physiology and Behavior, University of California Davis, Davis, United States
| | - Vincent C Castillo
- V Castillo, Department of Neurobiology, Physiology and Behavior, University of California Davis, Davis, United States
| | - Cynthia J Donaldson
- C Donaldson, Peptide Biology Laboratories, Salk Institute for Biological Studies, La Jolla, United States
| | - Marcus R Flisher
- M Flisher, Department of Neurobiology, Physiology and Behavior, University of California Davis, Davis, United States
| | - Ariana T Momen
- A Momen, Department of Neurobiology, Physiology and Behavior, University of California Davis, Davis, United States
| | - Alan Saghatelian
- A Saghatelian, Clayton Foundation Laboratories for Peptide Biology, Salk Institute for Biological Studies, La Jolla, United States
| | - Mark O Huising
- M Huising, Department of Neurobiology, Physiology and Behavior, University of California Davis, Davis, United States
| |
Collapse
|
3
|
Köberlin MS, Fan Y, Liu C, Chung M, Pinto AFM, Jackson PK, Saghatelian A, Meyer T. A fast-acting lipid checkpoint in G1 prevents mitotic defects. Nat Commun 2024; 15:2441. [PMID: 38499565 PMCID: PMC10948896 DOI: 10.1038/s41467-024-46696-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 03/06/2024] [Indexed: 03/20/2024] Open
Abstract
Lipid synthesis increases during the cell cycle to ensure sufficient membrane mass, but how insufficient synthesis restricts cell-cycle entry is not understood. Here, we identify a lipid checkpoint in G1 phase of the mammalian cell cycle by using live single-cell imaging, lipidome, and transcriptome analysis of a non-transformed cell. We show that synthesis of fatty acids in G1 not only increases lipid mass but extensively shifts the lipid composition to unsaturated phospholipids and neutral lipids. Strikingly, acute lowering of lipid synthesis rapidly activates the PERK/ATF4 endoplasmic reticulum (ER) stress pathway that blocks cell-cycle entry by increasing p21 levels, decreasing Cyclin D levels, and suppressing Retinoblastoma protein phosphorylation. Together, our study identifies a rapid anticipatory ER lipid checkpoint in G1 that prevents cells from starting the cell cycle as long as lipid synthesis is low, thereby preventing mitotic defects, which are triggered by low lipid synthesis much later in mitosis.
Collapse
Affiliation(s)
- Marielle S Köberlin
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
- Baxter Laboratory, Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
| | - Yilin Fan
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA
| | - Chad Liu
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Chan Zuckerberg Biohub, San Francisco, CA, 94111, USA
| | - Mingyu Chung
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Antonio F M Pinto
- Clayton Foundation Laboratories for Peptide Biology and Mass Spectrometry Core, Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Peter K Jackson
- Baxter Laboratory, Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Alan Saghatelian
- Clayton Foundation Laboratories for Peptide Biology and Mass Spectrometry Core, Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Tobias Meyer
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
- Department of Cell and Developmental Biology, Weill Cornell Medicine, New York, NY, 10065, USA.
| |
Collapse
|
4
|
Riecan M, Domanska V, Lupu C, Patel M, Vondrackova M, Rossmeisl M, Saghatelian A, Lupu F, Kuda O. Tissue-specific sex difference in the metabolism of fatty acid esters of hydroxy fatty acids. bioRxiv 2023:2023.11.15.567158. [PMID: 38014093 PMCID: PMC10680750 DOI: 10.1101/2023.11.15.567158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Fatty acid esters of hydroxy fatty acids (FAHFAs) are endogenous bioactive lipids known for their anti-inflammatory and anti-diabetic properties. Despite their therapeutic potential, little is known about the sex-specific variations in FAHFA metabolism. This study investigated the role of Androgen Dependent TFPI Regulating Protein (ADTRP), a FAHFA hydrolase. Additionally, tissue-specific differences in FAHFA levels, focusing on the perigonadal white adipose tissue (pgWAT), subcutaneous white adipose tissue (scWAT), brown adipose tissue (BAT), plasma, and liver, were evaluated using metabolomics and lipidomics. We found that female mice exhibited higher FAHFA levels in pgWAT, scWAT, and BAT compared to males. FAHFA levels were inversely related to Adtrp mRNA, which showed significantly lower expression in females compared with males in pgWAT and scWAT. However, no significant differences between the sexes were observed in plasma and liver FAHFA levels. Adtrp deletion had minimal impact on both sexes' metabolome and lipidome of pgWAT. However, we discovered higher endogenous levels of triacylglycerol estolides containing FAHFAs, a FAHFA metabolic reservoir, in the pgWAT of female mice. These findings suggest that sex-dependent differences in FAHFA levels occur primarily in specific WAT depots and may modulate local insulin sensitivity in adipocytes. However, further investigations are warranted to fully comprehend the underlying mechanisms and implications of sex effects on FAHFA metabolism in humans.
Collapse
Affiliation(s)
- Martin Riecan
- Metabolism of Bioactive Lipids, Institute of Physiology of the Czech Academy of Sciences, Videnska 1083, 14200 Prague, Czechia
| | - Veronika Domanska
- Metabolism of Bioactive Lipids, Institute of Physiology of the Czech Academy of Sciences, Videnska 1083, 14200 Prague, Czechia
| | - Cristina Lupu
- Cardiovascular Biology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
| | - Maulin Patel
- Cardiovascular Biology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
| | - Michaela Vondrackova
- Metabolism of Bioactive Lipids, Institute of Physiology of the Czech Academy of Sciences, Videnska 1083, 14200 Prague, Czechia
| | - Martin Rossmeisl
- Adipose Tissue Biology, Institute of Physiology of the Czech Academy of Sciences, Videnska 1083, 14200 Prague, Czechia
| | - Alan Saghatelian
- Clayton Foundation Laboratories for Peptide Biology, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Florea Lupu
- Cardiovascular Biology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
| | - Ondrej Kuda
- Metabolism of Bioactive Lipids, Institute of Physiology of the Czech Academy of Sciences, Videnska 1083, 14200 Prague, Czechia
| |
Collapse
|
5
|
Xie L, Bowman ME, Louie GV, Zhang C, Ardejani MS, Huang X, Chu Q, Donaldson CJ, Vaughan JM, Shan H, Powers ET, Kelly JW, Lyumkis D, Noel JP, Saghatelian A. Biochemistry and Protein Interactions of the CYREN Microprotein. Biochemistry 2023; 62:3050-3060. [PMID: 37813856 DOI: 10.1021/acs.biochem.3c00397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/11/2023]
Abstract
Over the past decade, advances in genomics have identified thousands of additional protein-coding small open reading frames (smORFs) missed by traditional gene finding approaches. These smORFs encode peptides and small proteins, commonly termed micropeptides or microproteins. Several of these newly discovered microproteins have biological functions and operate through interactions with proteins and protein complexes within the cell. CYREN1 is a characterized microprotein that regulates double-strand break repair in mammalian cells through interaction with Ku70/80 heterodimer. Ku70/80 binds to and stabilizes double-strand breaks and recruits the machinery needed for nonhomologous end join repair. In this study, we examined the biochemical properties of CYREN1 to better understand and explain its cellular protein interactions. Our findings support that CYREN1 is an intrinsically disordered microprotein and this disordered structure allows it to enriches several proteins, including a newly discovered interaction with SF3B1 via a distinct short linear motif (SLiMs) on CYREN1. Since many microproteins are predicted to be disordered, CYREN1 is an exemplar of how microproteins interact with other proteins and reveals an unknown scaffolding function of this microprotein that may link NHEJ and splicing.
Collapse
Affiliation(s)
- Lina Xie
- Clayton Foundation Peptide Biology Laboratories, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Marianne E Bowman
- Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Gordon V Louie
- Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Cheng Zhang
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Maziar S Ardejani
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Xuemei Huang
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92037, United States
| | - Qian Chu
- Department of Pharmacy, China Pharmaceutical University, Nanjing 210009, Jiangsu, China
| | - Cynthia J Donaldson
- Clayton Foundation Peptide Biology Laboratories, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Joan M Vaughan
- Clayton Foundation Peptide Biology Laboratories, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Huanqi Shan
- Clayton Foundation Peptide Biology Laboratories, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Evan T Powers
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Jeffery W Kelly
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Dimitry Lyumkis
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Joseph P Noel
- Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Alan Saghatelian
- Clayton Foundation Peptide Biology Laboratories, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, California 92037, United States
| |
Collapse
|
6
|
de Souza EV, Bookout AL, Barnes CA, Miller B, Machado P, Basso LA, Bizarro CV, Saghatelian A. The Integration of Proteogenomics and Ribosome Profiling Circumvents Key Limitations to Increase the Coverage and Confidence of Novel Microproteins. bioRxiv 2023:2023.09.27.559809. [PMID: 37808637 PMCID: PMC10557729 DOI: 10.1101/2023.09.27.559809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
There has been a dramatic increase in the identification of non-conical translation and a significant expansion of the protein-coding genome and proteome. Among the strategies used to identify novel small ORFs (smORFs), Ribosome profiling (Ribo-Seq) is the gold standard for the annotation of novel coding sequences by reporting on smORF translation. In Ribo-Seq, ribosome-protected footprints (RPFs) that map to multiple sites in the genome are computationally removed since they cannot unambiguously be assigned to a specific genomic location, or to a specific transcript in the case of multiple isoforms. Furthermore, RPFs necessarily result in short (25-34 nucleotides) reads, increasing the chance of ambiguous and multi-mapping alignments, such that smORFs that reside in these regions cannot be identified by Ribo-Seq. Here, we show that the inclusion of proteogenomics to create a Ribosome Profiling and Proteogenomics Pipeline (RP3) bypasses this limitation to identify a group of microprotein-encoding smORFs that are missed by current Ribo-Seq pipelines. Moreover, we show that the microproteins identified by RP3 have different sequence compositions from the ones identified by Ribo-Seq-only pipelines, which can affect proteomics identification. In aggregate, the development of RP3 maximizes the detection and confidence of protein-encoding smORFs and microproteins.
Collapse
|
7
|
Lazear MR, Remsberg JR, Jaeger MG, Rothamel K, Her HL, DeMeester KE, Njomen E, Hogg SJ, Rahman J, Whitby LR, Won SJ, Schafroth MA, Ogasawara D, Yokoyama M, Lindsey GL, Li H, Germain J, Barbas S, Vaughan J, Hanigan TW, Vartabedian VF, Reinhardt CJ, Dix MM, Koo SJ, Heo I, Teijaro JR, Simon GM, Ghosh B, Abdel-Wahab O, Ahn K, Saghatelian A, Melillo B, Schreiber SL, Yeo GW, Cravatt BF. Proteomic discovery of chemical probes that perturb protein complexes in human cells. Mol Cell 2023; 83:1725-1742.e12. [PMID: 37084731 PMCID: PMC10198961 DOI: 10.1016/j.molcel.2023.03.026] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 01/09/2023] [Accepted: 03/28/2023] [Indexed: 04/23/2023]
Abstract
Most human proteins lack chemical probes, and several large-scale and generalizable small-molecule binding assays have been introduced to address this problem. How compounds discovered in such "binding-first" assays affect protein function, nonetheless, often remains unclear. Here, we describe a "function-first" proteomic strategy that uses size exclusion chromatography (SEC) to assess the global impact of electrophilic compounds on protein complexes in human cells. Integrating the SEC data with cysteine-directed activity-based protein profiling identifies changes in protein-protein interactions that are caused by site-specific liganding events, including the stereoselective engagement of cysteines in PSME1 and SF3B1 that disrupt the PA28 proteasome regulatory complex and stabilize a dynamic state of the spliceosome, respectively. Our findings thus show how multidimensional proteomic analysis of focused libraries of electrophilic compounds can expedite the discovery of chemical probes with site-specific functional effects on protein complexes in human cells.
Collapse
Affiliation(s)
- Michael R Lazear
- Department of Chemistry, Scripps Research, La Jolla, CA 92037, USA
| | | | - Martin G Jaeger
- Department of Chemistry, Scripps Research, La Jolla, CA 92037, USA
| | - Katherine Rothamel
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Hsuan-Lin Her
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | | | - Evert Njomen
- Department of Chemistry, Scripps Research, La Jolla, CA 92037, USA
| | - Simon J Hogg
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA
| | - Jahan Rahman
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA
| | - Landon R Whitby
- Vividion Therapeutics, 5820 Nancy Ridge Drive, San Diego, CA 92121, USA
| | - Sang Joon Won
- Department of Chemistry, Scripps Research, La Jolla, CA 92037, USA
| | | | | | - Minoru Yokoyama
- Department of Chemistry, Scripps Research, La Jolla, CA 92037, USA
| | | | - Haoxin Li
- Department of Chemistry, Scripps Research, La Jolla, CA 92037, USA
| | - Jason Germain
- Department of Chemistry, Scripps Research, La Jolla, CA 92037, USA
| | - Sabrina Barbas
- Department of Chemistry, Scripps Research, La Jolla, CA 92037, USA
| | - Joan Vaughan
- Clayton Foundation Laboratories for Peptide Biology, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Thomas W Hanigan
- Department of Chemistry, Scripps Research, La Jolla, CA 92037, USA
| | - Vincent F Vartabedian
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA 92037, USA
| | | | - Melissa M Dix
- Department of Chemistry, Scripps Research, La Jolla, CA 92037, USA
| | - Seong Joo Koo
- Molecular and Cellular Pharmacology, Discovery Technologies and Molecular Pharmacology, Janssen Research and Development, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Inha Heo
- Molecular and Cellular Pharmacology, Discovery Technologies and Molecular Pharmacology, Janssen Research and Development, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - John R Teijaro
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA 92037, USA
| | - Gabriel M Simon
- Vividion Therapeutics, 5820 Nancy Ridge Drive, San Diego, CA 92121, USA
| | - Brahma Ghosh
- Discovery Chemistry, Janssen Research & Development, Spring House, PA 19477, USA
| | - Omar Abdel-Wahab
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA
| | - Kay Ahn
- Molecular and Cellular Pharmacology, Discovery Technologies and Molecular Pharmacology, Janssen Research and Development, Spring House, PA 19477, USA
| | - Alan Saghatelian
- Clayton Foundation Laboratories for Peptide Biology, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Bruno Melillo
- Department of Chemistry, Scripps Research, La Jolla, CA 92037, USA; Chemical Biology and Therapeutics Science Program, Broad Institute, Cambridge, MA 02142, USA
| | - Stuart L Schreiber
- Chemical Biology and Therapeutics Science Program, Broad Institute, Cambridge, MA 02142, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | | |
Collapse
|
8
|
Miller B, Kim SJ, Mehta HH, Cao K, Kumagai H, Thumaty N, Leelaprachakul N, Braniff RG, Jiao H, Vaughan J, Diedrich J, Saghatelian A, Arpawong TE, Crimmins EM, Ertekin-Taner N, Tubi MA, Hare ET, Braskie MN, Décarie-Spain L, Kanoski SE, Grodstein F, Bennett DA, Zhao L, Toga AW, Wan J, Yen K, Cohen P. Mitochondrial DNA variation in Alzheimer's disease reveals a unique microprotein called SHMOOSE. Mol Psychiatry 2023; 28:1813-1826. [PMID: 36127429 PMCID: PMC10027624 DOI: 10.1038/s41380-022-01769-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 08/15/2022] [Accepted: 08/26/2022] [Indexed: 01/22/2023]
Abstract
Mitochondrial DNA variants have previously associated with disease, but the underlying mechanisms have been largely elusive. Here, we report that mitochondrial SNP rs2853499 associated with Alzheimer's disease (AD), neuroimaging, and transcriptomics. We mapped rs2853499 to a novel mitochondrial small open reading frame called SHMOOSE with microprotein encoding potential. Indeed, we detected two unique SHMOOSE-derived peptide fragments in mitochondria by using mass spectrometry-the first unique mass spectrometry-based detection of a mitochondrial-encoded microprotein to date. Furthermore, cerebrospinal fluid (CSF) SHMOOSE levels in humans correlated with age, CSF tau, and brain white matter volume. We followed up on these genetic and biochemical findings by carrying out a series of functional experiments. SHMOOSE acted on the brain following intracerebroventricular administration, differentiated mitochondrial gene expression in multiple models, localized to mitochondria, bound the inner mitochondrial membrane protein mitofilin, and boosted mitochondrial oxygen consumption. Altogether, SHMOOSE has vast implications for the fields of neurobiology, Alzheimer's disease, and microproteins.
Collapse
Affiliation(s)
- Brendan Miller
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA
- Neuroscience Graduate Program, University of Southern California, Los Angeles, CA, USA
| | - Su-Jeong Kim
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA
| | - Hemal H Mehta
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA
| | - Kevin Cao
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA
| | - Hiroshi Kumagai
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA
| | - Neehar Thumaty
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA
| | - Naphada Leelaprachakul
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA
| | - Regina Gonzalez Braniff
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA
| | - Henry Jiao
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA
| | - Joan Vaughan
- Clayton Foundation Laboratories for Peptide Biology, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Jolene Diedrich
- Clayton Foundation Laboratories for Peptide Biology, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Alan Saghatelian
- Clayton Foundation Laboratories for Peptide Biology, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Thalida E Arpawong
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA
| | - Eileen M Crimmins
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA
| | | | - Meral A Tubi
- Imaging Genetics Center, Institute for Neuroimaging and Informatics, University of Southern California, Los Angeles, CA, USA
- Department of Neurology, University of Southern California, Los Angeles, CA, USA
| | - Evan T Hare
- Imaging Genetics Center, Institute for Neuroimaging and Informatics, University of Southern California, Los Angeles, CA, USA
- Department of Neurology, University of Southern California, Los Angeles, CA, USA
| | - Meredith N Braskie
- Imaging Genetics Center, Institute for Neuroimaging and Informatics, University of Southern California, Los Angeles, CA, USA
- Department of Neurology, University of Southern California, Los Angeles, CA, USA
| | - Léa Décarie-Spain
- Human and Evolutionary Biology Section, Department of Biological Sciences, Dornsife College of Letters, Arts and Sciences, University of Southern California, Los Angeles, CA, USA
| | - Scott E Kanoski
- Neuroscience Graduate Program, University of Southern California, Los Angeles, CA, USA
- Human and Evolutionary Biology Section, Department of Biological Sciences, Dornsife College of Letters, Arts and Sciences, University of Southern California, Los Angeles, CA, USA
| | - Francine Grodstein
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Lu Zhao
- Laboratory of Neuro Imaging, USC Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of University of Southern California, Los Angeles, CA, USA
| | - Arthur W Toga
- Laboratory of Neuro Imaging, USC Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of University of Southern California, Los Angeles, CA, USA
| | - Junxiang Wan
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA
| | - Kelvin Yen
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA
| | - Pinchas Cohen
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA.
| |
Collapse
|
9
|
Morgado-Palacin L, Brown JA, Martinez TF, Garcia-Pedrero JM, Forouhar F, Quinn SA, Reglero C, Vaughan J, Heydary YH, Donaldson C, Rodriguez-Perales S, Allonca E, Granda-Diaz R, Fernandez AF, Fraga MF, Kim AL, Santos-Juanes J, Owens DM, Rodrigo JP, Saghatelian A, Ferrando AA. The TINCR ubiquitin-like microprotein is a tumor suppressor in squamous cell carcinoma. Nat Commun 2023; 14:1328. [PMID: 36899004 PMCID: PMC10006087 DOI: 10.1038/s41467-023-36713-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 02/13/2023] [Indexed: 03/12/2023] Open
Abstract
The TINCR (Terminal differentiation-Induced Non-Coding RNA) gene is selectively expressed in epithelium tissues and is involved in the control of human epidermal differentiation and wound healing. Despite its initial report as a long non-coding RNA, the TINCR locus codes for a highly conserved ubiquitin-like microprotein associated with keratinocyte differentiation. Here we report the identification of TINCR as a tumor suppressor in squamous cell carcinoma (SCC). TINCR is upregulated by UV-induced DNA damage in a TP53-dependent manner in human keratinocytes. Decreased TINCR protein expression is prevalently found in skin and head and neck squamous cell tumors and TINCR expression suppresses the growth of SCC cells in vitro and in vivo. Consistently, Tincr knockout mice show accelerated tumor development following UVB skin carcinogenesis and increased penetrance of invasive SCCs. Finally, genetic analyses identify loss-of-function mutations and deletions encompassing the TINCR gene in SCC clinical samples supporting a tumor suppressor role in human cancer. Altogether, these results demonstrate a role for TINCR as protein coding tumor suppressor gene recurrently lost in squamous cell carcinomas.
Collapse
Affiliation(s)
| | - Jessie A Brown
- Institute for Cancer Genetics, Columbia University, New York, NY, USA
| | - Thomas F Martinez
- Department of Pharmaceutical Sciences, University of California, Irvine, CA, USA
| | - Juana M Garcia-Pedrero
- Department of Otolaryngology, Hospital Universitario Central de Asturias (HUCA), Oviedo, Spain.,Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain.,Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, Oviedo, Spain.,Ciber de Cáncer, CIBERONC, Madrid, Spain
| | - Farhad Forouhar
- Proteomics and Macromolecular Crystallography Shared Resource, Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA
| | - S Aidan Quinn
- Institute for Cancer Genetics, Columbia University, New York, NY, USA
| | - Clara Reglero
- Institute for Cancer Genetics, Columbia University, New York, NY, USA
| | - Joan Vaughan
- Clayton Foundation Laboratories for Peptide Biology, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Yasamin Hajy Heydary
- Department of Pharmaceutical Sciences, University of California, Irvine, CA, USA
| | - Cynthia Donaldson
- Clayton Foundation Laboratories for Peptide Biology, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Sandra Rodriguez-Perales
- Molecular Cytogenetics Group, Human Cancer Genetics Program, Centro Nacional de Investigaciones Oncológicas (CNIO), 28029, Madrid, Spain
| | - Eva Allonca
- Department of Otolaryngology, Hospital Universitario Central de Asturias (HUCA), Oviedo, Spain.,Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain.,Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, Oviedo, Spain
| | - Rocio Granda-Diaz
- Department of Otolaryngology, Hospital Universitario Central de Asturias (HUCA), Oviedo, Spain.,Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain.,Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, Oviedo, Spain.,Ciber de Cáncer, CIBERONC, Madrid, Spain
| | - Agustin F Fernandez
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain.,Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, Oviedo, Spain.,Cancer Epigenetics and Nanomedicine Laboratory, Nanomaterials and Nanotechnology Research Center (CINN-CSIC), El Entrego, Spain.,Department of Organisms and Systems Biology (B.O.S.), University of Oviedo, Oviedo, Spain.,Rare Diseases CIBER (ciberer) of the Carlos III Health Institute (ISCIII), Madrid, Spain
| | - Mario F Fraga
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain.,Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, Oviedo, Spain.,Cancer Epigenetics and Nanomedicine Laboratory, Nanomaterials and Nanotechnology Research Center (CINN-CSIC), El Entrego, Spain.,Department of Organisms and Systems Biology (B.O.S.), University of Oviedo, Oviedo, Spain.,Rare Diseases CIBER (ciberer) of the Carlos III Health Institute (ISCIII), Madrid, Spain
| | - Arianna L Kim
- Department of Dermatology, Columbia University Irving Medical Center, New York, NY, USA
| | - Jorge Santos-Juanes
- Department of Dermatology, Hospital Universitario Central de Asturias (HUCA), Oviedo, Asturias, Spain.,Dermatology Area, University of Oviedo Medical School, Oviedo, Asturias, Spain
| | - David M Owens
- Department of Dermatology, Columbia University Irving Medical Center, New York, NY, USA.,Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Juan P Rodrigo
- Department of Otolaryngology, Hospital Universitario Central de Asturias (HUCA), Oviedo, Spain.,Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain.,Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, Oviedo, Spain.,Ciber de Cáncer, CIBERONC, Madrid, Spain
| | - Alan Saghatelian
- Clayton Foundation Laboratories for Peptide Biology, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Adolfo A Ferrando
- Institute for Cancer Genetics, Columbia University, New York, NY, USA. .,Dermatology Area, University of Oviedo Medical School, Oviedo, Asturias, Spain. .,Department of Systems Biology, Columbia University, New York, NY, USA.
| |
Collapse
|
10
|
Tan D, Konduri S, Erikci Ertunc M, Zhang P, Wang J, Chang T, Pinto AFM, Rocha A, Donaldson CJ, Vaughan JM, Ludwig RG, Willey E, Iyer M, Gray PC, Maher P, Allen NJ, Zuchero JB, Dillin A, Mori MA, Kohama SG, Siegel D, Saghatelian A. A class of anti-inflammatory lipids decrease with aging in the central nervous system. Nat Chem Biol 2023; 19:187-197. [PMID: 36266352 PMCID: PMC9898107 DOI: 10.1038/s41589-022-01165-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 09/08/2022] [Indexed: 02/06/2023]
Abstract
Lipids contribute to the structure, development, and function of healthy brains. Dysregulated lipid metabolism is linked to aging and diseased brains. However, our understanding of lipid metabolism in aging brains remains limited. Here we examined the brain lipidome of mice across their lifespan using untargeted lipidomics. Co-expression network analysis highlighted a progressive decrease in 3-sulfogalactosyl diacylglycerols (SGDGs) and SGDG pathway members, including the potential degradation products lyso-SGDGs. SGDGs show an age-related decline specifically in the central nervous system and are associated with myelination. We also found that an SGDG dramatically suppresses LPS-induced gene expression and release of pro-inflammatory cytokines from macrophages and microglia by acting on the NF-κB pathway. The detection of SGDGs in human and macaque brains establishes their evolutionary conservation. This work enhances interest in SGDGs regarding their roles in aging and inflammatory diseases and highlights the complexity of the brain lipidome and potential biological functions in aging.
Collapse
Affiliation(s)
- Dan Tan
- Clayton Foundation Laboratories for Peptide Biology, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Srihari Konduri
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Meric Erikci Ertunc
- Clayton Foundation Laboratories for Peptide Biology, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Pan Zhang
- Department of Psychiatry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Justin Wang
- Clayton Foundation Laboratories for Peptide Biology, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Tina Chang
- Clayton Foundation Laboratories for Peptide Biology, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Antonio F M Pinto
- Clayton Foundation Laboratories for Peptide Biology, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Andrea Rocha
- Clayton Foundation Laboratories for Peptide Biology, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Cynthia J Donaldson
- Clayton Foundation Laboratories for Peptide Biology, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Joan M Vaughan
- Clayton Foundation Laboratories for Peptide Biology, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Raissa G Ludwig
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, Campinas, Brazil
| | - Elizabeth Willey
- Department of Molecular and Cellular Biology, Howard Hughes Medical Institute, The Glenn Center for Aging Research, University of California, Berkeley, Berkeley, CA, USA
| | - Manasi Iyer
- Department of Neurosurgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Peter C Gray
- Clayton Foundation Laboratories for Peptide Biology, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Pamela Maher
- Cellular Neurobiology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Nicola J Allen
- Molecular Neurobiology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - J Bradley Zuchero
- Department of Neurosurgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Andrew Dillin
- Department of Molecular and Cellular Biology, Howard Hughes Medical Institute, The Glenn Center for Aging Research, University of California, Berkeley, Berkeley, CA, USA
| | - Marcelo A Mori
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, Campinas, Brazil
| | - Steven G Kohama
- Oregon National Primate Research Center, Oregon Health and Science University, Portland, OR, USA
| | - Dionicio Siegel
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA.
| | - Alan Saghatelian
- Clayton Foundation Laboratories for Peptide Biology, Salk Institute for Biological Studies, La Jolla, CA, USA.
| |
Collapse
|
11
|
Martinez TF, Lyons-Abbott S, Bookout AL, De Souza EV, Donaldson C, Vaughan JM, Lau C, Abramov A, Baquero AF, Baquero K, Friedrich D, Huard J, Davis R, Kim B, Koch T, Mercer AJ, Misquith A, Murray SA, Perry S, Pino LK, Sanford C, Simon A, Zhang Y, Zipp G, Bizarro CV, Shokhirev MN, Whittle AJ, Searle BC, MacCoss MJ, Saghatelian A, Barnes CA. Profiling mouse brown and white adipocytes to identify metabolically relevant small ORFs and functional microproteins. Cell Metab 2023; 35:166-183.e11. [PMID: 36599300 PMCID: PMC9889109 DOI: 10.1016/j.cmet.2022.12.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 09/19/2022] [Accepted: 12/06/2022] [Indexed: 01/05/2023]
Abstract
Microproteins (MPs) are a potentially rich source of uncharacterized metabolic regulators. Here, we use ribosome profiling (Ribo-seq) to curate 3,877 unannotated MP-encoding small ORFs (smORFs) in primary brown, white, and beige mouse adipocytes. Of these, we validated 85 MPs by proteomics, including 33 circulating MPs in mouse plasma. Analyses of MP-encoding mRNAs under different physiological conditions (high-fat diet) revealed that numerous MPs are regulated in adipose tissue in vivo and are co-expressed with established metabolic genes. Furthermore, Ribo-seq provided evidence for the translation of Gm8773, which encodes a secreted MP that is homologous to human and chicken FAM237B. Gm8773 is highly expressed in the arcuate nucleus of the hypothalamus, and intracerebroventricular administration of recombinant mFAM237B showed orexigenic activity in obese mice. Together, these data highlight the value of this adipocyte MP database in identifying MPs with roles in fundamental metabolic and physiological processes such as feeding.
Collapse
Affiliation(s)
- Thomas F Martinez
- Department of Pharmaceutical Sciences, Department of Biological Chemistry, Chao Family Comprehensive Cancer Center, University of California, Irvine, Irvine, CA, USA
| | | | - Angie L Bookout
- Novo Nordisk Research Center Seattle, Inc., Seattle, WA, USA
| | - Eduardo V De Souza
- Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF) and Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Brazil; Programa de Pós-Graduação em Biologia Celular e Molecular, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul 90616-900, Brazil; Clayton Foundation Laboratories for Peptide Biology, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Cynthia Donaldson
- Clayton Foundation Laboratories for Peptide Biology, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Joan M Vaughan
- Clayton Foundation Laboratories for Peptide Biology, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Calvin Lau
- Clayton Foundation Laboratories for Peptide Biology, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Ariel Abramov
- Novo Nordisk Research Center Seattle, Inc., Seattle, WA, USA
| | - Arian F Baquero
- Novo Nordisk Research Center Seattle, Inc., Seattle, WA, USA
| | - Karalee Baquero
- Novo Nordisk Research Center Seattle, Inc., Seattle, WA, USA
| | - Dave Friedrich
- Novo Nordisk Research Center Seattle, Inc., Seattle, WA, USA
| | - Justin Huard
- Novo Nordisk Research Center Seattle, Inc., Seattle, WA, USA
| | - Ray Davis
- Novo Nordisk Research Center Seattle, Inc., Seattle, WA, USA
| | - Bong Kim
- Novo Nordisk Research Center Seattle, Inc., Seattle, WA, USA
| | - Ty Koch
- Novo Nordisk Research Center Seattle, Inc., Seattle, WA, USA
| | - Aaron J Mercer
- Novo Nordisk Research Center Seattle, Inc., Seattle, WA, USA
| | - Ayesha Misquith
- Novo Nordisk Research Center Seattle, Inc., Seattle, WA, USA
| | - Sara A Murray
- Novo Nordisk Research Center Seattle, Inc., Seattle, WA, USA
| | - Sakara Perry
- Novo Nordisk Research Center Seattle, Inc., Seattle, WA, USA
| | - Lindsay K Pino
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | | | - Alex Simon
- Novo Nordisk Research Center Seattle, Inc., Seattle, WA, USA
| | - Yu Zhang
- Novo Nordisk Research Center Seattle, Inc., Seattle, WA, USA
| | - Garrett Zipp
- Novo Nordisk Research Center Seattle, Inc., Seattle, WA, USA
| | - Cristiano V Bizarro
- Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF) and Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Brazil; Programa de Pós-Graduação em Biologia Celular e Molecular, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul 90616-900, Brazil
| | - Maxim N Shokhirev
- Razavi Newman Integrative Genomics and Bioinformatics Core, Salk Institute for Biological Studies, La Jolla, CA, USA
| | | | - Brian C Searle
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA
| | - Michael J MacCoss
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Alan Saghatelian
- Clayton Foundation Laboratories for Peptide Biology, Salk Institute for Biological Studies, La Jolla, CA, USA.
| | - Christopher A Barnes
- Novo Nordisk Research Center Seattle, Inc., Seattle, WA, USA; Velia Therapeutics, Inc., San Diego, CA, USA.
| |
Collapse
|
12
|
Faust B, Billesbølle CB, Suomivuori CM, Singh I, Zhang K, Hoppe N, Pinto AFM, Diedrich JK, Muftuoglu Y, Szkudlinski MW, Saghatelian A, Dror RO, Cheng Y, Manglik A. Autoantibody mimicry of hormone action at the thyrotropin receptor. Nature 2022; 609:846-853. [PMID: 35940205 PMCID: PMC9678024 DOI: 10.1038/s41586-022-05159-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Accepted: 07/28/2022] [Indexed: 11/08/2022]
Abstract
Thyroid hormones are vital in metabolism, growth and development1. Thyroid hormone synthesis is controlled by thyrotropin (TSH), which acts at the thyrotropin receptor (TSHR)2. In patients with Graves' disease, autoantibodies that activate the TSHR pathologically increase thyroid hormone activity3. How autoantibodies mimic thyrotropin function remains unclear. Here we determined cryo-electron microscopy structures of active and inactive TSHR. In inactive TSHR, the extracellular domain lies close to the membrane bilayer. Thyrotropin selects an upright orientation of the extracellular domain owing to steric clashes between a conserved hormone glycan and the membrane bilayer. An activating autoantibody from a patient with Graves' disease selects a similar upright orientation of the extracellular domain. Reorientation of the extracellular domain transduces a conformational change in the seven-transmembrane-segment domain via a conserved hinge domain, a tethered peptide agonist and a phospholipid that binds within the seven-transmembrane-segment domain. Rotation of the TSHR extracellular domain relative to the membrane bilayer is sufficient for receptor activation, revealing a shared mechanism for other glycoprotein hormone receptors that may also extend to other G-protein-coupled receptors with large extracellular domains.
Collapse
MESH Headings
- Cell Membrane/metabolism
- Cryoelectron Microscopy
- Graves Disease/immunology
- Graves Disease/metabolism
- Humans
- Immunoglobulins, Thyroid-Stimulating/chemistry
- Immunoglobulins, Thyroid-Stimulating/immunology
- Immunoglobulins, Thyroid-Stimulating/pharmacology
- Immunoglobulins, Thyroid-Stimulating/ultrastructure
- Phospholipids/metabolism
- Protein Domains
- Receptors, G-Protein-Coupled/agonists
- Receptors, G-Protein-Coupled/chemistry
- Receptors, G-Protein-Coupled/ultrastructure
- Receptors, Thyrotropin/agonists
- Receptors, Thyrotropin/chemistry
- Receptors, Thyrotropin/immunology
- Receptors, Thyrotropin/ultrastructure
- Rotation
- Thyrotropin/chemistry
- Thyrotropin/metabolism
- Thyrotropin/pharmacology
Collapse
Affiliation(s)
- Bryan Faust
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
- Biophysics Graduate Program, University of California, San Francisco, CA, USA
| | | | - Carl-Mikael Suomivuori
- Department of Computer Science, Stanford University, Stanford, CA, USA
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
- Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA, USA
| | - Isha Singh
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA
| | - Kaihua Zhang
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
| | - Nicholas Hoppe
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA
- Biophysics Graduate Program, University of California, San Francisco, CA, USA
| | - Antonio F M Pinto
- Mass Spectrometry Core for Proteomics and Metabolomics, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Jolene K Diedrich
- Mass Spectrometry Core for Proteomics and Metabolomics, Salk Institute for Biological Studies, La Jolla, CA, USA
| | | | | | - Alan Saghatelian
- Clayton Foundation Laboratory for Peptide Biology Lab, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Ron O Dror
- Department of Computer Science, Stanford University, Stanford, CA, USA
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
- Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA, USA
| | - Yifan Cheng
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA.
- Biophysics Graduate Program, University of California, San Francisco, CA, USA.
- Howard Hughes Medical Institute, University of California, San Francisco, CA, USA.
| | - Aashish Manglik
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA.
- Biophysics Graduate Program, University of California, San Francisco, CA, USA.
- Department of Anesthesia and Perioperative Care, University of California, San Francisco, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
| |
Collapse
|
13
|
Russell BJ, Brown SD, Siguenza N, Mai I, Saran AR, Lingaraju A, Maissy ES, Dantas Machado AC, Pinto AFM, Sanchez C, Rossitto LA, Miyamoto Y, Richter RA, Ho SB, Eckmann L, Hasty J, Gonzalez DJ, Saghatelian A, Knight R, Zarrinpar A. Intestinal transgene delivery with native E. coli chassis allows persistent physiological changes. Cell 2022; 185:3263-3277.e15. [PMID: 35931082 PMCID: PMC9464905 DOI: 10.1016/j.cell.2022.06.050] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 04/15/2022] [Accepted: 06/25/2022] [Indexed: 12/26/2022]
Abstract
Live bacterial therapeutics (LBTs) could reverse diseases by engrafting in the gut and providing persistent beneficial functions in the host. However, attempts to functionally manipulate the gut microbiome of conventionally raised (CR) hosts have been unsuccessful because engineered microbial organisms (i.e., chassis) have difficulty in colonizing the hostile luminal environment. In this proof-of-concept study, we use native bacteria as chassis for transgene delivery to impact CR host physiology. Native Escherichia coli bacteria isolated from the stool cultures of CR mice were modified to express functional genes. The reintroduction of these strains induces perpetual engraftment in the intestine. In addition, engineered native E. coli can induce functional changes that affect physiology of and reverse pathology in CR hosts months after administration. Thus, using native bacteria as chassis to “knock in” specific functions allows mechanistic studies of specific microbial activities in the microbiome of CR hosts and enables LBT with curative intent. Native E. coli strains isolated from mouse stool are genetically engineered for long-term engraftment in the conventional mouse gut and enable long-term systemic effects on the host, such as improvements in insulin sensitivity in mouse models of type 2 diabetes.
Collapse
Affiliation(s)
- Baylee J Russell
- Division of Gastroenterology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Steven D Brown
- Division of Gastroenterology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Nicole Siguenza
- Division of Gastroenterology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Irene Mai
- Division of Gastroenterology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Anand R Saran
- Division of Gastroenterology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Amulya Lingaraju
- Division of Gastroenterology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Erica S Maissy
- Division of Gastroenterology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Ana C Dantas Machado
- Division of Gastroenterology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Antonio F M Pinto
- Clayton Foundation Laboratories for Peptide Biology, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Concepcion Sanchez
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Leigh-Ana Rossitto
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Yukiko Miyamoto
- Division of Gastroenterology, University of California, San Diego, La Jolla, CA 92093, USA
| | - R Alexander Richter
- Division of Gastroenterology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Samuel B Ho
- Division of Gastroenterology, University of California, San Diego, La Jolla, CA 92093, USA; VA Health Sciences San Diego, La Jolla, CA 92161, USA
| | - Lars Eckmann
- Division of Gastroenterology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jeff Hasty
- BioCircuits Institute, University of California, San Diego, La Jolla, CA 92093, USA; Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA; Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA 92093, USA
| | - David J Gonzalez
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA; Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA 92093, USA
| | - Alan Saghatelian
- Clayton Foundation Laboratories for Peptide Biology, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Rob Knight
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA; Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA; Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA 92093, USA; Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Amir Zarrinpar
- Division of Gastroenterology, University of California, San Diego, La Jolla, CA 92093, USA; VA Health Sciences San Diego, La Jolla, CA 92161, USA; Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA 92093, USA.
| |
Collapse
|
14
|
Dantas Machado AC, Brown SD, Lingaraju A, Sivaganesh V, Martino C, Chaix A, Zhao P, Pinto AFM, Chang MW, Richter RA, Saghatelian A, Saltiel AR, Knight R, Panda S, Zarrinpar A. Diet and feeding pattern modulate diurnal dynamics of the ileal microbiome and transcriptome. Cell Rep 2022; 40:111008. [PMID: 35793637 PMCID: PMC9296000 DOI: 10.1016/j.celrep.2022.111008] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 03/28/2022] [Accepted: 06/03/2022] [Indexed: 12/30/2022] Open
Abstract
Compositional oscillations of the gut microbiome are essential for normal peripheral circadian rhythms, both of which are disrupted in diet-induced obesity (DIO). Although time-restricted feeding (TRF) maintains circadian synchrony and protects against DIO, its impact on the dynamics of the cecal gut microbiome is modest. Thus, other regions of the gut, particularly the ileum, the nexus for incretin and bile acid signaling, may play an important role in entraining peripheral circadian rhythms. We demonstrate the effect of diet and feeding rhythms on the ileal microbiome composition and transcriptome in mice. The dynamic rhythms of ileal microbiome composition and transcriptome are dampened in DIO. TRF partially restores diurnal rhythms of the ileal microbiome and transcriptome, increases GLP-1 release, and alters the ileal bile acid pool and farnesoid X receptor (FXR) signaling, which could explain how TRF exerts its metabolic benefits. Finally, we provide a web resource for exploration of ileal microbiome and transcriptome circadian data.
Collapse
Affiliation(s)
- Ana Carolina Dantas Machado
- Division of Gastroenterology, University of California, San Diego, 9500 Gilman Drive, MC 0983, La Jolla, CA, USA; Department of Medicine, University of California, San Diego, 9500 Gilman Drive, MC 0983, La Jolla, CA, USA
| | - Steven D Brown
- Division of Gastroenterology, University of California, San Diego, 9500 Gilman Drive, MC 0983, La Jolla, CA, USA; Department of Medicine, University of California, San Diego, 9500 Gilman Drive, MC 0983, La Jolla, CA, USA
| | - Amulya Lingaraju
- Division of Gastroenterology, University of California, San Diego, 9500 Gilman Drive, MC 0983, La Jolla, CA, USA; Department of Medicine, University of California, San Diego, 9500 Gilman Drive, MC 0983, La Jolla, CA, USA
| | - Vignesh Sivaganesh
- Division of Gastroenterology, University of California, San Diego, 9500 Gilman Drive, MC 0983, La Jolla, CA, USA; Department of Medicine, University of California, San Diego, 9500 Gilman Drive, MC 0983, La Jolla, CA, USA
| | - Cameron Martino
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, USA; Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA, USA; Center for Microbiome Innovation, University of California, San Diego, 9500 Gilman Drive, MC 0983, La Jolla, CA, USA
| | - Amandine Chaix
- Department of Nutrition and Integrative Physiology, University of Utah, Salt Lake City, UT, USA
| | - Peng Zhao
- Department of Medicine, University of California, San Diego, 9500 Gilman Drive, MC 0983, La Jolla, CA, USA; Division of Metabolism and Endocrinology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Antonio F M Pinto
- Clayton Foundation Laboratories for Peptide Biology, the Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Max W Chang
- Department of Medicine, University of California, San Diego, 9500 Gilman Drive, MC 0983, La Jolla, CA, USA
| | - R Alexander Richter
- Division of Gastroenterology, University of California, San Diego, 9500 Gilman Drive, MC 0983, La Jolla, CA, USA; Department of Medicine, University of California, San Diego, 9500 Gilman Drive, MC 0983, La Jolla, CA, USA
| | - Alan Saghatelian
- Clayton Foundation Laboratories for Peptide Biology, the Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Alan R Saltiel
- Department of Medicine, University of California, San Diego, 9500 Gilman Drive, MC 0983, La Jolla, CA, USA; Division of Metabolism and Endocrinology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA; Department of Pharmacology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA; Institute of Diabetes and Metabolic Health, University of California, San Diego, 9500 Gilman Drive, MC 0983, La Jolla, CA, USA
| | - Rob Knight
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, USA; Center for Microbiome Innovation, University of California, San Diego, 9500 Gilman Drive, MC 0983, La Jolla, CA, USA; Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA; Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Satchidananda Panda
- Regulatory Biology Laboratory, The Salk Institute, 10010 N. Torrey Pines Road, La Jolla, CA, USA
| | - Amir Zarrinpar
- Division of Gastroenterology, University of California, San Diego, 9500 Gilman Drive, MC 0983, La Jolla, CA, USA; Department of Medicine, University of California, San Diego, 9500 Gilman Drive, MC 0983, La Jolla, CA, USA; Center for Microbiome Innovation, University of California, San Diego, 9500 Gilman Drive, MC 0983, La Jolla, CA, USA; Institute of Diabetes and Metabolic Health, University of California, San Diego, 9500 Gilman Drive, MC 0983, La Jolla, CA, USA; VA Health Sciences, San Diego, La Jolla, CA, USA.
| |
Collapse
|
15
|
Mudge JM, Ruiz-Orera J, Prensner JR, Brunet MA, Calvet F, Jungreis I, Gonzalez JM, Magrane M, Martinez TF, Schulz JF, Yang YT, Albà MM, Aspden JL, Baranov PV, Bazzini AA, Bruford E, Martin MJ, Calviello L, Carvunis AR, Chen J, Couso JP, Deutsch EW, Flicek P, Frankish A, Gerstein M, Hubner N, Ingolia NT, Kellis M, Menschaert G, Moritz RL, Ohler U, Roucou X, Saghatelian A, Weissman JS, van Heesch S. Standardized annotation of translated open reading frames. Nat Biotechnol 2022; 40:994-999. [PMID: 35831657 PMCID: PMC9757701 DOI: 10.1038/s41587-022-01369-0] [Citation(s) in RCA: 61] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Jonathan M Mudge
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.
| | - Jorge Ruiz-Orera
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany.
| | - John R Prensner
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA.
| | - Marie A Brunet
- Department of Pediatrics, Medical Genetics Service, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Ferriol Calvet
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Irwin Jungreis
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA, USA
| | - Jose Manuel Gonzalez
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Michele Magrane
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Thomas F Martinez
- Clayton Foundation Laboratories for Peptide Biology, Salk Institute for Biological Studies, La Jolla, CA, USA
- Department of Pharmaceutical Sciences, University of California, Irvine, CA, USA
| | - Jana Felicitas Schulz
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Yucheng T Yang
- Program in Computational Biology & Bioinformatics, Yale University, New Haven, CT, USA
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, USA
| | - M Mar Albà
- Evolutionary Genomics Group, Research Programme on Biomedical Informatics, Hospital del Mar Research Institute (IMIM) and Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Julie L Aspden
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
- LeedsOmics, University of Leeds, Leeds, UK
| | - Pavel V Baranov
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Ariel A Bazzini
- Stowers Institute for Medical Research, Kansas City, MO, USA
- Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, KS, USA
| | - Elspeth Bruford
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Department of Haematology, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Maria Jesus Martin
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Lorenzo Calviello
- Functional Genomics Centre, Human Technopole, Milan, Italy
- Computational Biology Centre, Human Technopole, Milan, Italy
| | - Anne-Ruxandra Carvunis
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Pittsburgh Center for Evolutionary Biology and Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Jin Chen
- Department of Pharmacology and Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Juan Pablo Couso
- Centro Andaluz de Biologia del Desarrollo, CSIC-UPO, Seville, Spain
| | | | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Adam Frankish
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Mark Gerstein
- Program in Computational Biology & Bioinformatics, Yale University, New Haven, CT, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
- Department of Computer Science, Yale University, New Haven, CT, USA
- Department of Statistics & Data Science, Yale University, New Haven, CT, USA
| | - Norbert Hubner
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Charité-Universitätsmedizin, Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, Berlin, Germany
| | - Nicholas T Ingolia
- Department of Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, USA
| | - Manolis Kellis
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA, USA
| | - Gerben Menschaert
- Biobix, Lab of Bioinformatics and Computational Genomics, Department of Mathematical Modelling, Statistics and Bioinformatics, Ghent University, Ghent, Belgium
| | | | - Uwe Ohler
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Department of Biology, Humboldt-Universität zu Berlin, Berlin, Germany
- Department of Computer Science, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Xavier Roucou
- Department of Biochemistry and Functional Genomics, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Alan Saghatelian
- Clayton Foundation Laboratories for Peptide Biology, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Jonathan S Weissman
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | |
Collapse
|
16
|
Patel R, Santoro A, Hofer P, Tan D, Oberer M, Nelson AT, Konduri S, Siegel D, Zechner R, Saghatelian A, Kahn BB. ATGL is a biosynthetic enzyme for fatty acid esters of hydroxy fatty acids. Nature 2022; 606:968-975. [PMID: 35676490 PMCID: PMC9242854 DOI: 10.1038/s41586-022-04787-x] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 04/21/2022] [Indexed: 12/16/2022]
Abstract
Branched fatty acid (FA) esters of hydroxy FAs (HFAs; FAHFAs) are recently discovered lipids that are conserved from yeast to mammals1,2. A subfamily, palmitic acid esters of hydroxy stearic acids (PAHSAs), are anti-inflammatory and anti-diabetic1,3. Humans and mice with insulin resistance have lower PAHSA levels in subcutaneous adipose tissue and serum1. PAHSA administration improves glucose tolerance and insulin sensitivity and reduces inflammation in obesity, diabetes and immune-mediated diseases1,4-7. The enzyme(s) responsible for FAHFA biosynthesis in vivo remains unknown. Here we identified adipose triglyceride lipase (ATGL, also known as patatin-like phospholipase domain containing 2 (PNPLA2)) as a candidate biosynthetic enzyme for FAHFAs using chemical biology and proteomics. We discovered that recombinant ATGL uses a transacylation reaction that esterifies an HFA with a FA from triglyceride (TG) or diglyceride to produce FAHFAs. Overexpression of wild-type, but not catalytically dead, ATGL increases FAHFA biosynthesis. Chemical inhibition of ATGL or genetic deletion of Atgl inhibits FAHFA biosynthesis and reduces the levels of FAHFA and FAHFA-TG. Levels of endogenous and nascent FAHFAs and FAHFA-TGs are 80-90 per cent lower in adipose tissue of mice in which Atgl is knocked out specifically in the adipose tissue. Increasing TG levels by upregulating diacylglycerol acyltransferase (DGAT) activity promotes FAHFA biosynthesis, and decreasing DGAT activity inhibits it, reinforcing TGs as FAHFA precursors. ATGL biosynthetic transacylase activity is present in human adipose tissue underscoring its potential clinical relevance. In summary, we discovered the first, to our knowledge, biosynthetic enzyme that catalyses the formation of the FAHFA ester bond in mammals. Whereas ATGL lipase activity is well known, our data establish a paradigm shift demonstrating that ATGL transacylase activity is biologically important.
Collapse
Affiliation(s)
- Rucha Patel
- Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, USA
| | - Anna Santoro
- Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, USA
| | - Peter Hofer
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
| | - Dan Tan
- Clayton Foundation Laboratories for Peptide Biology, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Monika Oberer
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
| | - Andrew T Nelson
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California-San Diego, La Jolla, CA, USA
| | - Srihari Konduri
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California-San Diego, La Jolla, CA, USA
| | - Dionicio Siegel
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California-San Diego, La Jolla, CA, USA
| | - Rudolf Zechner
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
- BioTechMed-Graz, Graz, Austria
| | - Alan Saghatelian
- Clayton Foundation Laboratories for Peptide Biology, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Barbara B Kahn
- Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, USA.
| |
Collapse
|
17
|
Lewandowski D, Foik AT, Smidak R, Choi EH, Zhang J, Hoang T, Tworak A, Suh S, Leinonen H, Dong Z, Pinto AF, Tom E, Luu JC, Lee JY, Ma X, Bieberich E, Blackshaw S, Saghatelian A, Lyon DC, Skowronska-Krawczyk D, Tabaka M, Palczewski K. Inhibition of ceramide accumulation in AdipoR1-/- mice increases photoreceptor survival and improves vision. JCI Insight 2022; 7:156301. [PMID: 35015730 PMCID: PMC8876453 DOI: 10.1172/jci.insight.156301] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 01/05/2022] [Indexed: 11/20/2022] Open
Abstract
Adiponectin receptor 1 (ADIPOR1) is a lipid and glucose metabolism regulator that possesses intrinsic ceramidase activity. Mutations of the ADIPOR1 gene have been associated with nonsyndromic and syndromic retinitis pigmentosa. Here, we show that the absence of AdipoR1 in mice leads to progressive photoreceptor degeneration, significant reduction of electroretinogram amplitudes, decreased retinoid content in the retina, and reduced cone opsin expression. Single-cell RNA-Seq results indicate that ADIPOR1 encoded the most abundantly expressed ceramidase in mice and one of the 2 most highly expressed ceramidases in the human retina, next to acid ceramidase ASAH1. We discovered an accumulation of ceramides in the AdipoR1–/– retina, likely due to insufficient ceramidase activity for healthy retina function, resulting in photoreceptor death. Combined treatment with desipramine/L-cycloserine (DC) lowered ceramide levels and exerted a protective effect on photoreceptors in AdipoR1–/– mice. Moreover, we observed improvement in cone-mediated retinal function in the DC-treated animals. Lastly, we found that prolonged DC treatment corrected the electrical responses of the primary visual cortex to visual stimuli, approaching near-normal levels for some parameters. These results highlight the importance of ADIPOR1 ceramidase in the retina and show that pharmacological inhibition of ceramide generation can provide a therapeutic strategy for ADIPOR1-related retinopathy.
Collapse
Affiliation(s)
- Dominik Lewandowski
- Department of Ophthalmology, University of California, Irvine, Irvine, United States of America
| | - Andrzej T Foik
- International Center for Translational Eye Research, Institute of Physical Chemistry PAS, Warsaw, Poland
| | - Roman Smidak
- Department of Ophthalmology, University of California, Irvine, Irvine, United States of America
| | - Elliot H Choi
- Department of Pharmacology, Case Western Reserve University, Cleveland, United States of America
| | - Jianye Zhang
- Department of Ophthalmology, University of California, Irvine, Irvine, United States of America
| | - Thanh Hoang
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, United States of America
| | - Aleksander Tworak
- Department of Ophthalmology, University of California, Irvine, Irvine, United States of America
| | - Susie Suh
- Department of Pharmacology, Case Western Reserve University, Cleveland, United States of America
| | - Henri Leinonen
- Department of Ophthalmology, University of California, Irvine, Irvine, United States of America
| | - Zhiqian Dong
- Department of Medical Devices, Polgenix Inc., Cleveland, United States of America
| | - Antonio Fm Pinto
- Clayton Foundation Laboratories for Peptide Biology, Salk Institute for Biological Studies, La Jolla, United States of America
| | - Emily Tom
- Department of Ophthalmology, University of California, Irvine, Irvine, United States of America
| | - Jennings C Luu
- Department of Ophthalmology, University of California, Irvine, Irvine, United States of America
| | - Joan Y Lee
- MetroHealth Medical Center, Case Western Reserve University, Cleveland, United States of America
| | - Xiuli Ma
- Department of Medical Devices, Polgenix Inc, Cleveland, United States of America
| | - Erhard Bieberich
- Department of Physiology, University of Kentucky, Lexington, United States of America
| | - Seth Blackshaw
- Solomon H. Snyder Department of Neuroscience, John Hopkins School of Medicine, Baltimore, United States of America
| | - Alan Saghatelian
- Clayton Foundation Laboratories for Peptide Biology, Salk Institute for Biological Studies, La Jolla, United States of America
| | - David C Lyon
- Department of Anatomy and Neurobiology, University of California, Irvine, Irvine, United States of America
| | | | - Marcin Tabaka
- International Center for Translational Eye Research, Institute of Physical Chemistry PAS, Warsaw, Poland
| | - Krzysztof Palczewski
- Department of Ophthalmology, University of California, Irvine, Irvine, United States of America
| |
Collapse
|
18
|
Sancar G, Liu S, Gasser E, Alvarez JG, Moutos C, Kim K, van Zutphen T, Wang Y, Huddy TF, Ross B, Dai Y, Zepeda D, Collins B, Tilley E, Kolar MJ, Yu RT, Atkins AR, van Dijk TH, Saghatelian A, Jonker JW, Downes M, Evans RM. FGF1 and insulin control lipolysis by convergent pathways. Cell Metab 2022; 34:171-183.e6. [PMID: 34986332 PMCID: PMC8863067 DOI: 10.1016/j.cmet.2021.12.004] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 09/08/2021] [Accepted: 12/06/2021] [Indexed: 01/07/2023]
Abstract
Inexorable increases in insulin resistance, lipolysis, and hepatic glucose production (HGP) are hallmarks of type 2 diabetes. Previously, we showed that peripheral delivery of exogenous fibroblast growth factor 1 (FGF1) has robust anti-diabetic effects mediated by the adipose FGF receptor (FGFR) 1. However, its mechanism of action is not known. Here, we report that FGF1 acutely lowers HGP by suppressing adipose lipolysis. On a molecular level, FGF1 inhibits the cAMP-protein kinase A axis by activating phosphodiesterase 4D (PDE4D), which separates it mechanistically from the inhibitory actions of insulin via PDE3B. We identify Ser44 as an FGF1-induced regulatory phosphorylation site in PDE4D that is modulated by the feed-fast cycle. These findings establish the FGF1/PDE4 pathway as an alternate regulator of the adipose-HGP axis and identify FGF1 as an unrecognized regulator of fatty acid homeostasis.
Collapse
Affiliation(s)
- Gencer Sancar
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Sihao Liu
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Emanuel Gasser
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Jacqueline G Alvarez
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Christopher Moutos
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Kyeongkyu Kim
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Tim van Zutphen
- Section of Molecular Metabolism and Nutrition, Department of Pediatrics, University of Groningen, University Medical Center Groningen, 9713 GZ, Groningen, the Netherlands
| | - Yuhao Wang
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Timothy F Huddy
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Brittany Ross
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Yang Dai
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - David Zepeda
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Brett Collins
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Emma Tilley
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Matthew J Kolar
- Clayton Foundation Laboratories for Peptide Biology, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Ruth T Yu
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Annette R Atkins
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Theo H van Dijk
- Section of Molecular Metabolism and Nutrition, Department of Pediatrics, University of Groningen, University Medical Center Groningen, 9713 GZ, Groningen, the Netherlands
| | - Alan Saghatelian
- Clayton Foundation Laboratories for Peptide Biology, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Johan W Jonker
- Section of Molecular Metabolism and Nutrition, Department of Pediatrics, University of Groningen, University Medical Center Groningen, 9713 GZ, Groningen, the Netherlands
| | - Michael Downes
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
| | - Ronald M Evans
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
| |
Collapse
|
19
|
Aryal P, Syed I, Lee J, Patel R, Nelson AT, Siegel D, Saghatelian A, Kahn BB. Distinct biological activities of isomers from several families of branched fatty acid esters of hydroxy fatty acids (FAHFAs). J Lipid Res 2021; 62:100108. [PMID: 34418413 PMCID: PMC8479484 DOI: 10.1016/j.jlr.2021.100108] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 08/09/2021] [Accepted: 08/13/2021] [Indexed: 12/24/2022] Open
Abstract
Branched fatty acid esters of hydroxy fatty acids (FAHFAs) are endogenous lipids with antidiabetic and anti-inflammatory effects. Each FAHFA family consists of esters with different acyl chains and multiple isomers with branch points at different carbons. Some FAHFAs, including palmitic acid hydroxy stearic acids (PAHSAs), improve insulin sensitivity and glucose tolerance in mice by enhancing glucose-stimulated insulin secretion (GSIS), insulin-stimulated glucose transport, and insulin action to suppress hepatic glucose production and reducing adipose tissue inflammation. However, little is known about the biological effects of other FAHFAs. Here, we investigated whether PAHSAs, oleic acid hydroxy stearic acid, palmitoleic acid hydroxy stearic acid, and stearic acid hydroxy stearic acid potentiate GSIS in β-cells and human islets, insulin-stimulated glucose uptake in adipocytes, and anti-inflammatory effects in immune cells. We also investigated whether they activate G protein-coupled receptor 40, which mediates the effects of PAHSAs on insulin secretion and sensitivity in vivo. We show that many FAHFAs potentiate GSIS, activate G protein-coupled receptor 40, and attenuate LPS-induced chemokine and cytokine expression and secretion and phagocytosis in immune cells. However, fewer FAHFAs augment insulin-stimulated glucose uptake in adipocytes. S-9-PAHSA, but not R-9-PAHSA, potentiated GSIS and glucose uptake, while both stereoisomers had anti-inflammatory effects. FAHFAs containing unsaturated acyl chains with higher branching from the carboxylate head group are more likely to potentiate GSIS, whereas FAHFAs with lower branching are more likely to be anti-inflammatory. This study provides insight into the specificity of the biological actions of different FAHFAs and could lead to the development of FAHFAs to treat metabolic and immune-mediated diseases.
Collapse
Affiliation(s)
- Pratik Aryal
- Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, USA
| | - Ismail Syed
- Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, USA
| | - Jennifer Lee
- Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, USA
| | - Rucha Patel
- Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, USA
| | - Andrew T Nelson
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, USA
| | - Dionicio Siegel
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, USA
| | - Alan Saghatelian
- Clayton Foundation Laboratories for Peptide Biology, Salk Institute for Biological Studies, La Jolla, California, USA
| | - Barbara B Kahn
- Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, USA.
| |
Collapse
|
20
|
Sander CL, Sears AE, Pinto AF, Choi EH, Kahremany S, Gao F, Salom D, Jin H, Pardon E, Suh S, Dong Z, Steyaert J, Saghatelian A, Skowronska-Krawczyk D, Kiser PD, Palczewski K. Nano-scale resolution of native retinal rod disk membranes reveals differences in lipid composition. J Cell Biol 2021; 220:e202101063. [PMID: 34132745 PMCID: PMC8240855 DOI: 10.1083/jcb.202101063] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 04/26/2021] [Accepted: 05/18/2021] [Indexed: 02/07/2023] Open
Abstract
Photoreceptors rely on distinct membrane compartments to support their specialized function. Unlike protein localization, identification of critical differences in membrane content has not yet been expanded to lipids, due to the difficulty of isolating domain-specific samples. We have overcome this by using SMA to coimmunopurify membrane proteins and their native lipids from two regions of photoreceptor ROS disks. Each sample's copurified lipids were subjected to untargeted lipidomic and fatty acid analysis. Extensive differences between center (rhodopsin) and rim (ABCA4 and PRPH2/ROM1) samples included a lower PC to PE ratio and increased LC- and VLC-PUFAs in the center relative to the rim region, which was enriched in shorter, saturated FAs. The comparatively few differences between the two rim samples likely reflect specific protein-lipid interactions. High-resolution profiling of the ROS disk lipid composition gives new insights into how intricate membrane structure and protein activity are balanced within the ROS, and provides a model for future studies of other complex cellular structures.
Collapse
Affiliation(s)
- Christopher L. Sander
- Department of Pharmacology, Case Western Reserve University, Cleveland, OH
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California, Irvine, Irvine, CA
| | - Avery E. Sears
- Department of Pharmacology, Case Western Reserve University, Cleveland, OH
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California, Irvine, Irvine, CA
| | - Antonio F.M. Pinto
- Clayton Foundation Laboratories for Peptide Biology, Salk Institute for Biological Studies, La Jolla, CA
| | - Elliot H. Choi
- Department of Pharmacology, Case Western Reserve University, Cleveland, OH
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California, Irvine, Irvine, CA
| | - Shirin Kahremany
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California, Irvine, Irvine, CA
| | - Fangyuan Gao
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California, Irvine, Irvine, CA
| | - David Salom
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California, Irvine, Irvine, CA
| | - Hui Jin
- Department of Pharmacology, Case Western Reserve University, Cleveland, OH
| | - Els Pardon
- Vlaams Instituut voor Biotechnologie–Vrije Universiteit Brussel Center for Structural Biology, Vlaams Instituut voor Biotechnologie, Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | - Susie Suh
- Department of Pharmacology, Case Western Reserve University, Cleveland, OH
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California, Irvine, Irvine, CA
| | - Zhiqian Dong
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California, Irvine, Irvine, CA
| | - Jan Steyaert
- Vlaams Instituut voor Biotechnologie–Vrije Universiteit Brussel Center for Structural Biology, Vlaams Instituut voor Biotechnologie, Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | - Alan Saghatelian
- Clayton Foundation Laboratories for Peptide Biology, Salk Institute for Biological Studies, La Jolla, CA
| | - Dorota Skowronska-Krawczyk
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California, Irvine, Irvine, CA
- Department of Physiology and Biophysics, University of California, Irvine, Irvine, CA
| | - Philip D. Kiser
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California, Irvine, Irvine, CA
- Department of Physiology and Biophysics, University of California, Irvine, Irvine, CA
- Research Service, VA Long Beach Healthcare System, Long Beach, CA
| | - Krzysztof Palczewski
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California, Irvine, Irvine, CA
- Department of Physiology and Biophysics, University of California, Irvine, Irvine, CA
- Department of Chemistry, University of California, Irvine, Irvine, CA
| |
Collapse
|
21
|
Becuwe M, Bond LM, Pinto AFM, Boland S, Mejhert N, Elliott SD, Cicconet M, Graham MM, Liu XN, Ilkayeva O, Saghatelian A, Walther TC, Farese RV. FIT2 is an acyl-coenzyme A diphosphatase crucial for endoplasmic reticulum homeostasis. J Cell Biol 2021; 219:152082. [PMID: 32915949 PMCID: PMC7659722 DOI: 10.1083/jcb.202006111] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 07/16/2020] [Accepted: 07/17/2020] [Indexed: 12/13/2022] Open
Abstract
The endoplasmic reticulum is a cellular hub of lipid metabolism, coordinating lipid synthesis with continuous changes in metabolic flux. Maintaining ER lipid homeostasis despite these fluctuations is crucial to cell function and viability. Here, we identify a novel mechanism that is crucial for normal ER lipid metabolism and protects the ER from dysfunction. We identify the molecular function of the evolutionarily conserved ER protein FIT2 as a fatty acyl–coenzyme A (CoA) diphosphatase that hydrolyzes fatty acyl–CoA to yield acyl 4′-phosphopantetheine. This activity of FIT2, which is predicted to be active in the ER lumen, is required in yeast and mammalian cells for maintaining ER structure, protecting against ER stress, and enabling normal lipid storage in lipid droplets. Our findings thus solve the long-standing mystery of the molecular function of FIT2 and highlight the maintenance of optimal fatty acyl–CoA levels as key to ER homeostasis.
Collapse
Affiliation(s)
- Michel Becuwe
- Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, MA.,Department of Cell Biology, Harvard Medical School, Boston, MA.,Broad Institute of MIT and Harvard, Cambridge, MA
| | - Laura M Bond
- Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, MA.,Department of Cell Biology, Harvard Medical School, Boston, MA.,Broad Institute of MIT and Harvard, Cambridge, MA
| | - Antonio F M Pinto
- Clayton Foundation Laboratories for Peptide Biology, Salk Institute for Biological Studies, La Jolla, CA
| | - Sebastian Boland
- Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, MA.,Department of Cell Biology, Harvard Medical School, Boston, MA.,Broad Institute of MIT and Harvard, Cambridge, MA
| | - Niklas Mejhert
- Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, MA.,Department of Cell Biology, Harvard Medical School, Boston, MA.,Broad Institute of MIT and Harvard, Cambridge, MA
| | - Shane D Elliott
- Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, MA.,Department of Cell Biology, Harvard Medical School, Boston, MA.,Broad Institute of MIT and Harvard, Cambridge, MA.,Howard Hughes Medical Institute, Boston, MA
| | - Marcelo Cicconet
- Image and Data Analysis Core, Harvard Medical School, Boston, MA
| | - Morven M Graham
- Center for Cellular and Molecular Imaging, Department of Cell Biology, Yale School of Medicine, New Haven, CT
| | - Xinran N Liu
- Center for Cellular and Molecular Imaging, Department of Cell Biology, Yale School of Medicine, New Haven, CT
| | - Olga Ilkayeva
- Departments of Medicine and Pharmacology and Cancer Biology, Sarah W. Stedman Nutrition and Metabolism Center and Duke Molecular Physiology Institute, Duke University, Durham, NC
| | - Alan Saghatelian
- Clayton Foundation Laboratories for Peptide Biology, Salk Institute for Biological Studies, La Jolla, CA
| | - Tobias C Walther
- Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, MA.,Department of Cell Biology, Harvard Medical School, Boston, MA.,Broad Institute of MIT and Harvard, Cambridge, MA.,Howard Hughes Medical Institute, Boston, MA
| | - Robert V Farese
- Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, MA.,Department of Cell Biology, Harvard Medical School, Boston, MA.,Broad Institute of MIT and Harvard, Cambridge, MA
| |
Collapse
|
22
|
Abstract
N-acyl amino acids are a class of biologically active lipids that control thermogenesis, and their biosynthesis is facilitated by PM20D1. In this issue of Cell Chemical Biology, Kim et al. (2020) identify a lipoprotein-albumin network in the blood that regulates physiological levels of N-acyl amino acids.
Collapse
Affiliation(s)
- Alan Saghatelian
- The Salk Institute for Biological Studies, Clayton Foundation Laboratories for Peptide Biology, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA.
| |
Collapse
|
23
|
Muthusamy T, Cordes T, Handzlik MK, You L, Lim EW, Gengatharan J, Pinto AFM, Badur MG, Kolar MJ, Wallace M, Saghatelian A, Metallo CM. Serine restriction alters sphingolipid diversity to constrain tumour growth. Nature 2020; 586:790-795. [PMID: 32788725 PMCID: PMC7606299 DOI: 10.1038/s41586-020-2609-x] [Citation(s) in RCA: 141] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 05/11/2020] [Indexed: 11/22/2022]
Abstract
Serine, glycine, and other non-essential amino acids are critical for tumor progression, and strategies to limit their availability are emerging as potential cancer therapies1–3. However, the molecular mechanisms driving this response remain unclear, and the impact on lipid metabolism is relatively unexplored. Serine palmitoyltransferase (SPT) catalyzes the de novo biosynthesis of sphingolipids but also produces non-canonical 1-deoxysphingolipids (doxSLs) when using alanine as a substrate4,5. DoxSLs accumulate in the context of SPTLC1 or SPTLC2 mutations6,7 or low serine availability8,9 to drive neuropathy, and deoxysphinganine (doxSA) has been investigated as an anti-cancer agent10. Here we exploit amino acid metabolism and SPT promiscuity to modulate the endogenous synthesis of toxic doxSLs and slow tumor progression. Anchorage-independent growth reprograms a metabolic network involving serine, alanine, and pyruvate resulting in increased susceptibility to endogenous doxSL synthesis. Targeting the mitochondrial pyruvate carrier (MPC) promotes alanine oxidation to mitigate doxSL synthesis and improves spheroid growth, while direct inhibition of doxSL synthesis drives similar phenotypes. Restriction of dietary serine/glycine potently induces accumulation of doxSLs in xenografts while decreasing tumor growth. Pharmacological modulation of SPT rescues xenograft growth on serine/glycine-restricted diets, while reduction of circulating serine by inhibition of phosphoglycerate dehydrogenase (PHGDH) leads to doxSL accumulation and mitigates tumor growth. SPT promiscuity therefore links serine and mitochondrial alanine metabolism to membrane lipid diversity, which sensitizes tumors to metabolic stress.
Collapse
Affiliation(s)
| | - Thekla Cordes
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Michal K Handzlik
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Le You
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Esther W Lim
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Jivani Gengatharan
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Antonio F M Pinto
- Mass Spectrometry Core, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Mehmet G Badur
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Matthew J Kolar
- Clayton Foundation Laboratories for Peptide Biology, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Martina Wallace
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Alan Saghatelian
- Clayton Foundation Laboratories for Peptide Biology, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Christian M Metallo
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA. .,Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA.
| |
Collapse
|
24
|
Charron MJ, Williams L, Seki Y, Du XQ, Chaurasia B, Saghatelian A, Summers SA, Katz EB, Vuguin PM, Reznik SE. Antioxidant Effects of N-Acetylcysteine Prevent Programmed Metabolic Disease in Mice. Diabetes 2020; 69:1650-1661. [PMID: 32444367 PMCID: PMC7372077 DOI: 10.2337/db19-1129] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 05/20/2020] [Indexed: 12/14/2022]
Abstract
An adverse maternal in utero and lactation environment can program offspring for increased risk for metabolic disease. The aim of this study was to determine whether N-acetylcysteine (NAC), an anti-inflammatory antioxidant, attenuates programmed susceptibility to obesity and insulin resistance in offspring of mothers on a high-fat diet (HFD) during pregnancy. CD1 female mice were acutely fed a standard breeding chow or HFD. NAC was added to the drinking water (1 g/kg) of the treatment cohorts from embryonic day 0.5 until the end of lactation. NAC treatment normalized HFD-induced maternal weight gain and oxidative stress, improved the maternal lipidome, and prevented maternal leptin resistance. These favorable changes in the in utero environment normalized postnatal growth, decreased white adipose tissue (WAT) and hepatic fat, improved glucose and insulin tolerance and antioxidant capacity, reduced leptin and insulin, and increased adiponectin in HFD offspring. The lifelong metabolic improvements in the offspring were accompanied by reductions in proinflammatory gene expression in liver and WAT and increased thermogenic gene expression in brown adipose tissue. These results, for the first time, provide a mechanistic rationale for how NAC can prevent the onset of metabolic disease in the offspring of mothers who consume a typical Western HFD.
Collapse
Affiliation(s)
- Maureen J Charron
- Department of Biochemistry, Albert Einstein College of Medicine, New York, NY
- Department of Medicine and Fleischer Institute for Diabetes and Metabolism, Albert Einstein College of Medicine, New York, NY
- Department of Obstetrics & Gynecology and Women's Health, Albert Einstein College of Medicine, New York, NY
| | - Lyda Williams
- Department of Biochemistry, Albert Einstein College of Medicine, New York, NY
| | - Yoshinori Seki
- Department of Biochemistry, Albert Einstein College of Medicine, New York, NY
| | - Xiu Quan Du
- Department of Biochemistry, Albert Einstein College of Medicine, New York, NY
| | - Bhagirath Chaurasia
- Department of Nutrition and Integrative Physiology, The University of Utah, Salt Lake City, UT
| | - Alan Saghatelian
- Clayton Foundation Laboratories for Peptide Biology, Salk Institute for Biological Studies, La Jolla, CA
| | - Scott A Summers
- Department of Nutrition and Integrative Physiology, The University of Utah, Salt Lake City, UT
| | - Ellen B Katz
- Department of Biochemistry, Albert Einstein College of Medicine, New York, NY
| | - Patricia M Vuguin
- Department of Pediatrics, Columbia University Vagelos College of Physicians & Surgeons, New York, NY
| | - Sandra E Reznik
- Department of Obstetrics & Gynecology and Women's Health, Albert Einstein College of Medicine, New York, NY
- Department of Pathology, Albert Einstein College of Medicine, New York, NY
- Department of Pharmaceutical Sciences, St. John's University, New York, NY
| |
Collapse
|
25
|
Affiliation(s)
- Thomas F Martinez
- Clayton Foundation Laboratories for Peptide Biology, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, California 92037-1002, United States
| | - Joan Vaughan
- Clayton Foundation Laboratories for Peptide Biology, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, California 92037-1002, United States
| | - Alan Saghatelian
- Clayton Foundation Laboratories for Peptide Biology, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, California 92037-1002, United States
| |
Collapse
|
26
|
Ertunc ME, Kok BP, Parsons WH, Wang JG, Tan D, Donaldson CJ, Pinto AM, Vaughan JM, Ngo N, Lum KM, Henry CL, Coppola AR, Niphakis MJ, Cravatt BF, Saez E, Saghatelian A. Role of AIG1 and ADTRP in Endogenous FAHFA Regulation. FASEB J 2020. [DOI: 10.1096/fasebj.2020.34.s1.04337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | | | | | | | - Dan Tan
- Salk Institute for Biological Studies
| | | | | | | | - Nhi Ngo
- Lundbeck La Jolla Research Center
| | | | | | | | | | | | | | | |
Collapse
|
27
|
Martinez TF, Chu Q, Donaldson C, Tan D, Shokhirev MN, Saghatelian A. Accurate Annotation of Protein‐coding Small Open Reading Frames in the Human Genome. FASEB J 2020. [DOI: 10.1096/fasebj.2020.34.s1.03051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | - Qian Chu
- Salk Institute for Biological Studies
| | | | - Dan Tan
- Salk Institute for Biological Studies
| | | | | |
Collapse
|
28
|
Chu Q, Martinez TF, Novak SW, Donaldson CJ, Tan D, Vaughan JM, Chang T, Diedrich JK, Andrade L, Kim A, Zhang T, Manor U, Saghatelian A. Regulation of the ER stress response by a mitochondrial microprotein. FASEB J 2020. [DOI: 10.1096/fasebj.2020.34.s1.04094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Qian Chu
- Salk Institute for Biological Studies
| | | | | | | | - Dan Tan
- Salk Institute for Biological Studies
| | | | | | | | | | | | | | - Uri Manor
- Salk Institute for Biological Studies
| | | |
Collapse
|
29
|
Erikci Ertunc M, Kok BP, Parsons WH, Wang JG, Tan D, Donaldson CJ, Pinto AFM, Vaughan JM, Ngo N, Lum KM, Henry CL, Coppola AR, Niphakis MJ, Cravatt BF, Saez E, Saghatelian A. AIG1 and ADTRP are endogenous hydrolases of fatty acid esters of hydroxy fatty acids (FAHFAs) in mice. J Biol Chem 2020; 295:5891-5905. [PMID: 32152231 DOI: 10.1074/jbc.ra119.012145] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 02/27/2020] [Indexed: 12/14/2022] Open
Abstract
Fatty acid esters of hydroxy fatty acids (FAHFAs) are a newly discovered class of signaling lipids with anti-inflammatory and anti-diabetic properties. However, the endogenous regulation of FAHFAs remains a pressing but unanswered question. Here, using MS-based FAHFA hydrolysis assays, LC-MS-based lipidomics analyses, and activity-based protein profiling, we found that androgen-induced gene 1 (AIG1) and androgen-dependent TFPI-regulating protein (ADTRP), two threonine hydrolases, control FAHFA levels in vivo in both genetic and pharmacologic mouse models. Tissues from mice lacking ADTRP (Adtrp-KO), or both AIG1 and ADTRP (DKO) had higher concentrations of FAHFAs particularly isomers with the ester bond at the 9th carbon due to decreased FAHFA hydrolysis activity. The levels of other lipid classes were unaltered indicating that AIG1 and ADTRP specifically hydrolyze FAHFAs. Complementing these genetic studies, we also identified a dual AIG1/ADTRP inhibitor, ABD-110207, which is active in vivo Acute treatment of WT mice with ABD-110207 resulted in elevated FAHFA levels, further supporting the notion that AIG1 and ADTRP activity control endogenous FAHFA levels. However, loss of AIG1/ADTRP did not mimic the changes associated with pharmacologically administered FAHFAs on extent of upregulation of FAHFA levels, glucose tolerance, or insulin sensitivity in mice, indicating that therapeutic strategies should weigh more on FAHFA administration. Together, these findings identify AIG1 and ADTRP as the first endogenous FAHFA hydrolases identified and provide critical genetic and chemical tools for further characterization of these enzymes and endogenous FAHFAs to unravel their physiological functions and roles in health and disease.
Collapse
Affiliation(s)
- Meric Erikci Ertunc
- Clayton Foundation Laboratories for Peptide Biology, The Salk Institute for Biological Studies, La Jolla, California 92037
| | - Bernard P Kok
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California 92037
| | - William H Parsons
- Department of Chemistry and Biochemistry, Oberlin College, Oberlin, Ohio 44074
| | - Justin G Wang
- Clayton Foundation Laboratories for Peptide Biology, The Salk Institute for Biological Studies, La Jolla, California 92037
| | - Dan Tan
- Clayton Foundation Laboratories for Peptide Biology, The Salk Institute for Biological Studies, La Jolla, California 92037
| | - Cynthia J Donaldson
- Clayton Foundation Laboratories for Peptide Biology, The Salk Institute for Biological Studies, La Jolla, California 92037
| | - Antonio F M Pinto
- Clayton Foundation Laboratories for Peptide Biology, The Salk Institute for Biological Studies, La Jolla, California 92037
| | - Joan M Vaughan
- Clayton Foundation Laboratories for Peptide Biology, The Salk Institute for Biological Studies, La Jolla, California 92037
| | - Nhi Ngo
- Lundbeck La Jolla Research Center, Inc., San Diego, California 92121
| | - Kenneth M Lum
- Lundbeck La Jolla Research Center, Inc., San Diego, California 92121
| | - Cassandra L Henry
- Lundbeck La Jolla Research Center, Inc., San Diego, California 92121
| | - Aundrea R Coppola
- Lundbeck La Jolla Research Center, Inc., San Diego, California 92121
| | - Micah J Niphakis
- Lundbeck La Jolla Research Center, Inc., San Diego, California 92121
| | - Benjamin F Cravatt
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037
| | - Enrique Saez
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California 92037
| | - Alan Saghatelian
- Clayton Foundation Laboratories for Peptide Biology, The Salk Institute for Biological Studies, La Jolla, California 92037.
| |
Collapse
|
30
|
Chen D, Chao DL, Rocha L, Kolar M, Nguyen Huu VA, Krawczyk M, Dasyani M, Wang T, Jafari M, Jabari M, Ross KD, Saghatelian A, Hamilton BA, Zhang K, Skowronska‐Krawczyk D. The lipid elongation enzyme ELOVL2 is a molecular regulator of aging in the retina. Aging Cell 2020; 19:e13100. [PMID: 31943697 PMCID: PMC6996962 DOI: 10.1111/acel.13100] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 11/22/2019] [Accepted: 12/12/2019] [Indexed: 12/31/2022] Open
Abstract
Methylation of the regulatory region of the elongation of very‐long‐chain fatty acids‐like 2 (ELOVL2) gene, an enzyme involved in elongation of long‐chain polyunsaturated fatty acids, is one of the most robust biomarkers of human age, but the critical question of whether ELOVL2 plays a functional role in molecular aging has not been resolved. Here, we report that Elovl2 regulates age‐associated functional and anatomical aging in vivo, focusing on mouse retina, with direct relevance to age‐related eye diseases. We show that an age‐related decrease in Elovl2 expression is associated with increased DNA methylation of its promoter. Reversal of Elovl2 promoter hypermethylation in vivo through intravitreal injection of 5‐Aza‐2’‐deoxycytidine (5‐Aza‐dc) leads to increased Elovl2 expression and rescue of age‐related decline in visual function. Mice carrying a point mutation C234W that disrupts Elovl2‐specific enzymatic activity show electrophysiological characteristics of premature visual decline, as well as early appearance of autofluorescent deposits, well‐established markers of aging in the mouse retina. Finally, we find deposits underneath the retinal pigment epithelium in Elovl2 mutant mice, containing components found in human drusen, a pathologic hallmark of age related macular degeneration. These findings indicate that ELOVL2 activity regulates aging in mouse retina, provide a molecular link between polyunsaturated fatty acids elongation and visual function, and suggest novel therapeutic strategies for the treatment of age‐related eye diseases.
Collapse
Affiliation(s)
- Daniel Chen
- Shiley Eye Institute Viterbi Family Department of Ophthalmology University of California San Diego La Jolla CA USA
| | - Daniel L. Chao
- Shiley Eye Institute Viterbi Family Department of Ophthalmology University of California San Diego La Jolla CA USA
| | - Lorena Rocha
- Shiley Eye Institute Viterbi Family Department of Ophthalmology University of California San Diego La Jolla CA USA
| | - Matthew Kolar
- The Salk Institute for Biological StudiesClayton Foundation Laboratories for Peptide BiologyLa Jolla CA USA
| | - Viet Anh Nguyen Huu
- Shiley Eye Institute Viterbi Family Department of Ophthalmology University of California San Diego La Jolla CA USA
| | - Michal Krawczyk
- Shiley Eye Institute Viterbi Family Department of Ophthalmology University of California San Diego La Jolla CA USA
| | - Manish Dasyani
- Shiley Eye Institute Viterbi Family Department of Ophthalmology University of California San Diego La Jolla CA USA
| | - Tina Wang
- Department of Medicine University of California San Diego La Jolla CA USA
| | - Maryam Jafari
- Shiley Eye Institute Viterbi Family Department of Ophthalmology University of California San Diego La Jolla CA USA
| | - Mary Jabari
- Shiley Eye Institute Viterbi Family Department of Ophthalmology University of California San Diego La Jolla CA USA
| | - Kevin D. Ross
- Department of Cellular and Molecular Medicine University of California San Diego La Jolla CA USA
| | - Alan Saghatelian
- The Salk Institute for Biological StudiesClayton Foundation Laboratories for Peptide BiologyLa Jolla CA USA
| | - Bruce A. Hamilton
- Department of Cellular and Molecular Medicine University of California San Diego La Jolla CA USA
- Institute for Genomic Medicine University of California San Diego La Jolla CA USA
| | - Kang Zhang
- Shiley Eye Institute Viterbi Family Department of Ophthalmology University of California San Diego La Jolla CA USA
| | - Dorota Skowronska‐Krawczyk
- Shiley Eye Institute Viterbi Family Department of Ophthalmology University of California San Diego La Jolla CA USA
- Atkinson Laboratory for Regenerative Medicine University of California San Diego La Jolla CA USA
| |
Collapse
|
31
|
Martinez TF, Chu Q, Donaldson C, Tan D, Shokhirev MN, Saghatelian A. Accurate annotation of human protein-coding small open reading frames. Nat Chem Biol 2019; 16:458-468. [PMID: 31819274 PMCID: PMC7085969 DOI: 10.1038/s41589-019-0425-0] [Citation(s) in RCA: 103] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 11/01/2019] [Indexed: 12/13/2022]
Abstract
Functional protein-coding small open reading frames (smORFs) are emerging as an important class of genes. However, the number of translated smORFs in the human genome is unclear because proteogenomic methods are not sensitive enough, and, as we show, Ribo-Seq strategies require additional measures to ensure comprehensive and accurate smORF annotation. Here, we integrate de novo transcriptome assembly and Ribo-Seq into an improved workflow that overcomes obstacles with previous methods to more confidently annotate thousands of smORFs. Evolutionary conservation analyses suggest that hundreds of smORF-encoded microproteins are likely functional. Additionally, many smORFs are regulated during fundamental biological processes, such as cell stress. Peptides derived from smORFs are also detectable on human leukocyte antigen complexes, revealing smORFs as a source of antigens. Thus, by including additional validation into our smORF annotation workflow, we accurately identify thousands of unannotated translated smORFs that will provide a rich pool of unexplored, functional human genes.
Collapse
Affiliation(s)
- Thomas F Martinez
- Clayton Foundation Laboratories for Peptide Biology, Salk Institute for Biological Studies, La Jolla, CA, USA.
| | - Qian Chu
- Clayton Foundation Laboratories for Peptide Biology, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Cynthia Donaldson
- Clayton Foundation Laboratories for Peptide Biology, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Dan Tan
- Clayton Foundation Laboratories for Peptide Biology, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Maxim N Shokhirev
- Razavi Newman Integrative Genomics Bioinformatics Core, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Alan Saghatelian
- Clayton Foundation Laboratories for Peptide Biology, Salk Institute for Biological Studies, La Jolla, CA, USA.
| |
Collapse
|
32
|
Chu Q, Martinez TF, Novak SW, Donaldson CJ, Tan D, Vaughan JM, Chang T, Diedrich JK, Andrade L, Kim A, Zhang T, Manor U, Saghatelian A. Regulation of the ER stress response by a mitochondrial microprotein. Nat Commun 2019; 10:4883. [PMID: 31653868 PMCID: PMC6814811 DOI: 10.1038/s41467-019-12816-z] [Citation(s) in RCA: 99] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 09/13/2019] [Indexed: 12/14/2022] Open
Abstract
Cellular homeostasis relies on having dedicated and coordinated responses to a variety of stresses. The accumulation of unfolded proteins in the endoplasmic reticulum (ER) is a common stress that triggers a conserved pathway called the unfolded protein response (UPR) that mitigates damage, and dysregulation of UPR underlies several debilitating diseases. Here, we discover that a previously uncharacterized 54-amino acid microprotein PIGBOS regulates UPR. PIGBOS localizes to the mitochondrial outer membrane where it interacts with the ER protein CLCC1 at ER–mitochondria contact sites. Functional studies reveal that the loss of PIGBOS leads to heightened UPR and increased cell death. The characterization of PIGBOS reveals an undiscovered role for a mitochondrial protein, in this case a microprotein, in the regulation of UPR originating in the ER. This study demonstrates microproteins to be an unappreciated class of genes that are critical for inter-organelle communication, homeostasis, and cell survival. Cells trigger an unfolded protein response (UPR) in the endoplasmic reticulum, but its regulation by mitochondria is unclear. Here, the authors report a 54-residue microprotein PIGBOS that participates in inter-organelle contact between the endoplasmic reticulum and the mitochondria and may regulate UPR.
Collapse
Affiliation(s)
- Qian Chu
- The Salk Institute for Biological Studies, Clayton Foundation Laboratories for Peptide Biology, 10010N. Torrey Pines Rd, La Jolla, CA, 92037, USA
| | - Thomas F Martinez
- The Salk Institute for Biological Studies, Clayton Foundation Laboratories for Peptide Biology, 10010N. Torrey Pines Rd, La Jolla, CA, 92037, USA
| | - Sammy Weiser Novak
- The Salk Institute for Biological Studies, Waitt Advanced Biophotonics Center, 10010N. Torrey Pines Rd, La Jolla, CA, 92037, USA
| | - Cynthia J Donaldson
- The Salk Institute for Biological Studies, Clayton Foundation Laboratories for Peptide Biology, 10010N. Torrey Pines Rd, La Jolla, CA, 92037, USA
| | - Dan Tan
- The Salk Institute for Biological Studies, Clayton Foundation Laboratories for Peptide Biology, 10010N. Torrey Pines Rd, La Jolla, CA, 92037, USA
| | - Joan M Vaughan
- The Salk Institute for Biological Studies, Clayton Foundation Laboratories for Peptide Biology, 10010N. Torrey Pines Rd, La Jolla, CA, 92037, USA
| | - Tina Chang
- The Salk Institute for Biological Studies, Clayton Foundation Laboratories for Peptide Biology, 10010N. Torrey Pines Rd, La Jolla, CA, 92037, USA
| | - Jolene K Diedrich
- The Salk Institute for Biological Studies, Clayton Foundation Laboratories for Peptide Biology, 10010N. Torrey Pines Rd, La Jolla, CA, 92037, USA
| | - Leo Andrade
- The Salk Institute for Biological Studies, Waitt Advanced Biophotonics Center, 10010N. Torrey Pines Rd, La Jolla, CA, 92037, USA
| | - Andrew Kim
- The Salk Institute for Biological Studies, Clayton Foundation Laboratories for Peptide Biology, 10010N. Torrey Pines Rd, La Jolla, CA, 92037, USA
| | - Tong Zhang
- The Salk Institute for Biological Studies, Waitt Advanced Biophotonics Center, 10010N. Torrey Pines Rd, La Jolla, CA, 92037, USA
| | - Uri Manor
- The Salk Institute for Biological Studies, Waitt Advanced Biophotonics Center, 10010N. Torrey Pines Rd, La Jolla, CA, 92037, USA.
| | - Alan Saghatelian
- The Salk Institute for Biological Studies, Clayton Foundation Laboratories for Peptide Biology, 10010N. Torrey Pines Rd, La Jolla, CA, 92037, USA.
| |
Collapse
|
33
|
Zhou P, Santoro A, Peroni OD, Nelson AT, Saghatelian A, Siegel D, Kahn BB. PAHSAs enhance hepatic and systemic insulin sensitivity through direct and indirect mechanisms. J Clin Invest 2019; 129:4138-4150. [PMID: 31449056 PMCID: PMC6763232 DOI: 10.1172/jci127092] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Accepted: 06/24/2019] [Indexed: 12/30/2022] Open
Abstract
Palmitic acid esters of hydroxy stearic acids (PAHSAs) are bioactive lipids with antiinflammatory and antidiabetic effects. PAHSAs reduce ambient glycemia and improve glucose tolerance and insulin sensitivity in insulin-resistant aged chow- and high-fat diet-fed (HFD-fed) mice. Here, we aimed to determine the mechanisms by which PAHSAs improve insulin sensitivity. Both acute and chronic PAHSA treatment enhanced the action of insulin to suppress endogenous glucose production (EGP) in chow- and HFD-fed mice. Moreover, chronic PAHSA treatment augmented insulin-stimulated glucose uptake in glycolytic muscle and heart in HFD-fed mice. The mechanisms by which PAHSAs enhanced hepatic insulin sensitivity included direct and indirect actions involving intertissue communication between adipose tissue and liver. PAHSAs inhibited lipolysis directly in WAT explants and enhanced the action of insulin to suppress lipolysis during the clamp in vivo. Preventing the reduction of free fatty acids during the clamp with Intralipid infusion reduced PAHSAs' effects on EGP in HFD-fed mice but not in chow-fed mice. Direct hepatic actions of PAHSAs may also be important, as PAHSAs inhibited basal and glucagon-stimulated EGP directly in isolated hepatocytes through a cAMP-dependent pathway involving Gαi protein-coupled receptors. Thus, this study advances our understanding of PAHSA biology and the physiologic mechanisms by which PAHSAs exert beneficial metabolic effects.
Collapse
Affiliation(s)
- Peng Zhou
- Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts, USA
| | - Anna Santoro
- Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts, USA
| | - Odile D. Peroni
- Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts, USA
| | - Andrew T. Nelson
- Skaggs School of Pharmacy and Pharmaceutical Sciences, UCSD, La Jolla, California, USA
| | - Alan Saghatelian
- Clayton Foundation Laboratories for Peptide Biology, Helmsley Center for Genomic Medicine, Salk Institute for Biological Studies, La Jolla, California, USA
| | - Dionicio Siegel
- Skaggs School of Pharmacy and Pharmaceutical Sciences, UCSD, La Jolla, California, USA
| | - Barbara B. Kahn
- Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts, USA
| |
Collapse
|
34
|
Wang H, Kolar MJ, Chang T, Rizo J, Konduri S, McNerlin C, Saghatelian A, Siegel D. Stereochemistry of Linoleic Acid Esters of Hydroxy Linoleic Acids. Org Lett 2019; 21:8080-8084. [DOI: 10.1021/acs.orglett.9b03054] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Huijing Wang
- Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, 9500 Gilman Drive, La Jolla, California 92093-0934, United States
| | - Matthew J. Kolar
- Clayton Foundation Laboratories for Peptide Biology, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, California 92037-1002, United States
| | - Tina Chang
- Clayton Foundation Laboratories for Peptide Biology, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, California 92037-1002, United States
| | - José Rizo
- Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, 9500 Gilman Drive, La Jolla, California 92093-0934, United States
| | - Srihari Konduri
- Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, 9500 Gilman Drive, La Jolla, California 92093-0934, United States
| | - Clare McNerlin
- Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, 9500 Gilman Drive, La Jolla, California 92093-0934, United States
| | - Alan Saghatelian
- Clayton Foundation Laboratories for Peptide Biology, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, California 92037-1002, United States
| | - Dionicio Siegel
- Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, 9500 Gilman Drive, La Jolla, California 92093-0934, United States
| |
Collapse
|
35
|
Syed I, Rubin de Celis MF, Mohan JF, Moraes-Vieira PM, Vijayakumar A, Nelson AT, Siegel D, Saghatelian A, Mathis D, Kahn BB. PAHSAs attenuate immune responses and promote β cell survival in autoimmune diabetic mice. J Clin Invest 2019; 129:3717-3731. [PMID: 31380811 PMCID: PMC6715391 DOI: 10.1172/jci122445] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 06/04/2019] [Indexed: 12/15/2022] Open
Abstract
Palmitic acid esters of hydroxy stearic acids (PAHSAs) are endogenous antidiabetic and antiinflammatory lipids. Here, we show that PAHSAs protect against type 1 diabetes (T1D) and promote β cell survival and function. Daily oral PAHSA administration to nonobese diabetic (NOD) mice delayed the onset of T1D and markedly reduced the incidence of T1D, whether PAHSAs were started before or after insulitis was established. PAHSAs reduced T and B cell infiltration and CD4+ and CD8+ T cell activation, while increasing Treg activation in pancreata of NOD mice. PAHSAs promoted β cell proliferation in both NOD mice and MIN6 cells and increased the number of β cells in NOD mice. PAHSAs attenuated cytokine-induced apoptotic and necrotic β cell death and increased β cell viability. The mechanism appears to involve a reduction of ER stress and MAPK signaling, since PAHSAs lowered ER stress in NOD mice, suppressed thapsigargin-induced PARP cleavage in human islets, and attenuated ERK1/2 and JNK1/2 activation in MIN6 cells. This appeared to be mediated in part by glucagon-like peptide 1 receptor (GLP-1R) and not the G protein-coupled receptor GPR40. PAHSAs also prevented impairment of glucose-stimulated insulin secretion and improved glucose tolerance in NOD mice. Thus, PAHSAs delayed the onset of T1D and reduced its incidence by attenuating immune responses and exerting direct protective effects on β cell survival and function.
Collapse
Affiliation(s)
- Ismail Syed
- Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts, USA
| | - Maria F. Rubin de Celis
- Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts, USA
| | - James F. Mohan
- Division of Immunology, Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Pedro M. Moraes-Vieira
- Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts, USA
| | - Archana Vijayakumar
- Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts, USA
| | - Andrew T. Nelson
- Skaggs School of Pharmacy and Pharmaceutical Sciences, UCSD, La Jolla, California, USA
| | - Dionicio Siegel
- Skaggs School of Pharmacy and Pharmaceutical Sciences, UCSD, La Jolla, California, USA
| | - Alan Saghatelian
- Clayton Foundation Laboratories for Peptide Biology, Helmsley Center for Genomic Medicine, Salk Institute for Biological Studies, La Jolla, California, USA
| | - Diane Mathis
- Division of Immunology, Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Barbara B. Kahn
- Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts, USA
| |
Collapse
|
36
|
Kolar MJ, Konduri S, Chang T, Wang H, McNerlin C, Ohlsson L, Härröd M, Siegel D, Saghatelian A. Linoleic acid esters of hydroxy linoleic acids are anti-inflammatory lipids found in plants and mammals. J Biol Chem 2019; 294:10698-10707. [PMID: 31152059 DOI: 10.1074/jbc.ra118.006956] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2018] [Revised: 05/29/2019] [Indexed: 11/06/2022] Open
Abstract
Fatty acid esters of hydroxy fatty acids (FAHFAs) are a recently discovered class of biologically active lipids. Here we identify the linoleic acid ester of 13-hydroxy linoleic acid (13-LAHLA) as an anti-inflammatory lipid. An oat oil fraction and FAHFA-enriched extract from this fraction showed anti-inflammatory activity in a lipopolysaccharide-induced cytokine secretion assay. Structural studies identified three LAHLA isomers (15-, 13-, and 9-LAHLA) as being the most abundant FAHFAs in the oat oil fraction. Of these LAHLAs, 13-LAHLA is the most abundant LAHLA isomer in human serum after ingestion of liposomes made of fractionated oat oil, and it is also the most abundant endogenous LAHLA in mouse and human adipose tissue. As a result, we chemically synthesized 13-LAHLA for biological assays. 13-LAHLA suppresses lipopolysaccharide-stimulated secretion of cytokines and expression of pro-inflammatory genes. These studies identify LAHLAs as an evolutionarily conserved lipid with anti-inflammatory activity in mammalian cells.
Collapse
Affiliation(s)
- Matthew J Kolar
- From the Clayton Foundation Laboratories for Peptide Biology, Salk Institute for Biological Studies, La Jolla, California 92037
| | - Srihari Konduri
- the Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California 92093-0934
| | - Tina Chang
- From the Clayton Foundation Laboratories for Peptide Biology, Salk Institute for Biological Studies, La Jolla, California 92037
| | - Huijing Wang
- the Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California 92093-0934
| | - Clare McNerlin
- the Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California 92093-0934
| | - Lena Ohlsson
- the Division of Experimental Vascular Research, Department of Clinical Sciences, Lund University, Box 117, 221 00 Lund, Sweden, and
| | - Magnus Härröd
- Härröd Research, Frans Persons väg 6, 40229 Gothenburg, Sweden
| | - Dionicio Siegel
- the Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California 92093-0934,
| | - Alan Saghatelian
- From the Clayton Foundation Laboratories for Peptide Biology, Salk Institute for Biological Studies, La Jolla, California 92037,
| |
Collapse
|
37
|
Tan D, Ertunc ME, Konduri S, Zhang J, Pinto AM, Chu Q, Kahn BB, Siegel D, Saghatelian A. Discovery of FAHFA-Containing Triacylglycerols and Their Metabolic Regulation. J Am Chem Soc 2019; 141:8798-8806. [PMID: 31056915 DOI: 10.1021/jacs.9b00045] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
FAHFAs are a class of bioactive lipids, which show great promise for treating diabetes and inflammatory diseases. Deciphering the metabolic pathways that regulate endogenous FAHFA levels is critical for developing diagnostic and therapeutic strategies. However, it remains unclear how FAHFAs are metabolized in cells or tissues. Here, we investigate whether FAHFAs can be incorporated into other lipid classes and identify a novel class of endogenous lipids, FAHFA-containing triacylglycerols (FAHFA-TGs), which contain a FAHFA group esterified to the glycerol backbone. Isotope-labeled FAHFAs are incorporated into FAHFA-TGs when added to differentiated adipocytes, which implies the existence of enzymes and metabolic pathways capable of synthesizing these lipids. Induction of lipolysis (i.e., triacylglycerol hydrolysis) in adipocytes is associated with marked increases in nonesterified FAHFA levels, demonstrating that FAHFA-TGs breakdown is a regulator of cellular FAHFA levels. To quantify FAHFA levels in FAHFA-TGs and determine their regioisomeric distributions, we developed a mild alkaline hydrolysis method that liberates FAHFAs from triacylglycerols for easier detection. FAHFA-TG concentrations are greater than 100-fold than that of nonesterified FAHFAs, indicating that FAHFA-TGs are a major reservoir of FAHFAs in cells and tissues. The discovery of FAHFA-TGs reveals a new branch of TG and FAHFA metabolism with potential roles in metabolic health and regulation of inflammation.
Collapse
Affiliation(s)
- Dan Tan
- Clayton Foundation Laboratories for Peptide Biology , Salk Institute for Biological Studies , 10010 North Torrey Pines Road , La Jolla , California 92037-1002 , United States
| | - Meric Erikci Ertunc
- Clayton Foundation Laboratories for Peptide Biology , Salk Institute for Biological Studies , 10010 North Torrey Pines Road , La Jolla , California 92037-1002 , United States
| | - Srihari Konduri
- Skaggs School of Pharmacy and Pharmaceutical Sciences , University of California-San Diego , 9500 Gilman Drive , La Jolla , California 92093-0934 , United States
| | - Justin Zhang
- Skaggs School of Pharmacy and Pharmaceutical Sciences , University of California-San Diego , 9500 Gilman Drive , La Jolla , California 92093-0934 , United States
| | - Antonio M Pinto
- Clayton Foundation Laboratories for Peptide Biology , Salk Institute for Biological Studies , 10010 North Torrey Pines Road , La Jolla , California 92037-1002 , United States
| | - Qian Chu
- Clayton Foundation Laboratories for Peptide Biology , Salk Institute for Biological Studies , 10010 North Torrey Pines Road , La Jolla , California 92037-1002 , United States
| | - Barbara B Kahn
- Division of Endocrinology, Diabetes and Metabolism, Department of Medicine , Beth Israel Deaconess Medical Center, Harvard Medical School , Boston , Massachusetts 02215 , United States
| | - Dionicio Siegel
- Skaggs School of Pharmacy and Pharmaceutical Sciences , University of California-San Diego , 9500 Gilman Drive , La Jolla , California 92093-0934 , United States
| | - Alan Saghatelian
- Clayton Foundation Laboratories for Peptide Biology , Salk Institute for Biological Studies , 10010 North Torrey Pines Road , La Jolla , California 92037-1002 , United States
| |
Collapse
|
38
|
Wang H, Chang T, Konduri S, Huang J, Saghatelian A, Siegel D. Synthesis of chemically edited derivatives of the endogenous regulator of inflammation 9-PAHSA. J Antibiot (Tokyo) 2019; 72:498-506. [PMID: 30988370 DOI: 10.1038/s41429-019-0180-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 03/14/2019] [Accepted: 03/18/2019] [Indexed: 02/07/2023]
Abstract
Fatty acid esters of hydroxy fatty acids (FAHFAs) are a growing class of natural products found in organisms ranging from plants to humans. The roles these endogenous derivatives of fatty acids play in biology and their novel pathways for controlling inflammation have increased our understanding of basic human physiology. FAHFAs incorporate diverse fatty acids into their structures, however, given their recent discovery non-natural derivatives have not been a focus and as a result structure-activity relationships remain unknown. The importance of the long chain hydrocarbons extending from the ester linkage as they relate to anti-inflammatory activity is unknown. Herein the systematic removal of carbons from either the hydroxy fatty acid or fatty acid regions of the most studied FAHFA, palmitic acid ester of 9-hydroxystearic acid (9-PAHSA), was achieved and these synthetic, abridged analogs were tested for their ability to attenuate IL-6 production. Reduction of the carbon chain lengths of the 9-hydroxystearic acid portion or palmitic acid hydrocarbon chain resulted in lower molecular weight analogs that maintained anti-inflammatory activity or in one case enhanced activity.
Collapse
Affiliation(s)
- Huijing Wang
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0934, USA
| | - Tina Chang
- Clayton Foundation Laboratories for Peptide Biology, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA, 92037-1002, USA
| | - Srihari Konduri
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0934, USA
| | - Jianbo Huang
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0934, USA
| | - Alan Saghatelian
- Clayton Foundation Laboratories for Peptide Biology, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA, 92037-1002, USA
| | - Dionicio Siegel
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0934, USA.
| |
Collapse
|
39
|
Choi SH, Martinez TF, Kim S, Donaldson C, Shokhirev MN, Saghatelian A, Jones KA. CDK12 phosphorylates 4E-BP1 to enable mTORC1-dependent translation and mitotic genome stability. Genes Dev 2019; 33:418-435. [PMID: 30819820 PMCID: PMC6446539 DOI: 10.1101/gad.322339.118] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 01/22/2019] [Indexed: 01/23/2023]
Abstract
Here, Choi et al. show that CDK12, the RNA polymerase II C-terminal domain kinase, which regulates genome stability, expression of DNA repair genes, and cancer cell drug resistance, also phosphorylates the mRNA 5′ cap-binding repressor 4E-BP1 to promote translation of mTORC1-dependent mRNAs. Using RIP-seq and Ribo-seq, the authors found that CDK12 regulates binding of eIF4G to many mTORC1 target mRNAs, and identified specific CDK12 “translation-only” target mRNAs. The RNA polymerase II (RNAPII) C-terminal domain kinase, CDK12, regulates genome stability, expression of DNA repair genes, and cancer cell resistance to chemotherapy and immunotherapy. In addition to its role in mRNA biosynthesis of DNA repair genes, we show here that CDK12 phosphorylates the mRNA 5′ cap-binding repressor, 4E-BP1, to promote translation of mTORC1-dependent mRNAs. In particular, we found that phosphorylation of 4E-BP1 by mTORC1 (T37 and T46) facilitates subsequent CDK12 phosphorylation at two Ser–Pro sites (S65 and T70) that control the exchange of 4E-BP1 with eIF4G at the 5′ cap of CHK1 and other target mRNAs. RNA immunoprecipitation coupled with deep sequencing (RIP-seq) revealed that CDK12 regulates release of 4E-BP1, and binding of eIF4G, to many mTORC1 target mRNAs, including those needed for MYC transformation. Genome-wide ribosome profiling (Ribo-seq) further identified specific CDK12 “translation-only” target mRNAs, including many mTORC1 target mRNAs as well as many subunits of mitotic and centromere/centrosome complexes. Accordingly, confocal imaging analyses revealed severe chromosome misalignment, bridging, and segregation defects in cells deprived of CDK12 or CCNK. We conclude that the nuclear RNAPII-CTD kinase CDK12 cooperates with mTORC1, and controls a specialized translation network that is essential for mitotic chromosome stability.
Collapse
Affiliation(s)
- Seung H Choi
- Regulatory Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Thomas F Martinez
- Clayton Foundation Laboratory for Peptide Biology, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Seongjae Kim
- Molecular Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Cynthia Donaldson
- Clayton Foundation Laboratory for Peptide Biology, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Maxim N Shokhirev
- Razavi Newman Integrative Genomics and Bioinformatics Core, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Alan Saghatelian
- Clayton Foundation Laboratory for Peptide Biology, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Katherine A Jones
- Regulatory Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
| |
Collapse
|
40
|
Affiliation(s)
- Qian Chu
- Clayton Foundation Laboratories for Peptide Biology , Salk Institute for Biological Studies , 10010 North Torrey Pines Road , La Jolla , California 92037-1002 , United States
| | - Alan Saghatelian
- Clayton Foundation Laboratories for Peptide Biology , Salk Institute for Biological Studies , 10010 North Torrey Pines Road , La Jolla , California 92037-1002 , United States
| |
Collapse
|
41
|
Rathore A, Martinez TF, Chu Q, Saghatelian A. Small, but mighty? Searching for human microproteins and their potential for understanding health and disease. Expert Rev Proteomics 2018; 15:963-965. [PMID: 30415582 DOI: 10.1080/14789450.2018.1547194] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Annie Rathore
- a Clayton Foundation Laboratories for Peptide Biology , The Salk Institute for Biological Studies , La Jolla , CA , USA
| | - Thomas F Martinez
- a Clayton Foundation Laboratories for Peptide Biology , The Salk Institute for Biological Studies , La Jolla , CA , USA
| | - Qian Chu
- a Clayton Foundation Laboratories for Peptide Biology , The Salk Institute for Biological Studies , La Jolla , CA , USA
| | - Alan Saghatelian
- a Clayton Foundation Laboratories for Peptide Biology , The Salk Institute for Biological Studies , La Jolla , CA , USA
| |
Collapse
|
42
|
Syed I, Lee J, Peroni OD, Yore MM, Moraes-Vieira PM, Santoro A, Wellenstein K, Smith U, McGraw TE, Saghatelian A, Kahn BB. Methodological Issues in Studying PAHSA Biology: Masking PAHSA Effects. Cell Metab 2018; 28:543-546. [PMID: 30244974 PMCID: PMC6542592 DOI: 10.1016/j.cmet.2018.09.007] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 08/30/2018] [Accepted: 09/05/2018] [Indexed: 11/29/2022]
Abstract
PAHSAs are anti-diabetic and anti-inflammatory lipids. Syed et al. identify numerous experimental differences that likely account for the failure of Pflimlin et al. to observe PAHSA beneficial effects. The differences include different HFDs resulting in minimal/no glucose intolerance, different assay conditions, an LC-MS protocol that was not validated, and use of olive oil, a bioactive nutrient that improves glucose tolerance, as a vehicle.
Collapse
Affiliation(s)
- Ismail Syed
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, 330 Brookline Avenue, Boston, MA 02215, USA
| | - Jennifer Lee
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, 330 Brookline Avenue, Boston, MA 02215, USA
| | - Odile D Peroni
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, 330 Brookline Avenue, Boston, MA 02215, USA
| | - Mark M Yore
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, 330 Brookline Avenue, Boston, MA 02215, USA
| | - Pedro M Moraes-Vieira
- Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, University of Campinas, Campinas-SP 13083-970, Brazil
| | - Anna Santoro
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, 330 Brookline Avenue, Boston, MA 02215, USA
| | - Kerry Wellenstein
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, 330 Brookline Avenue, Boston, MA 02215, USA
| | - Ulf Smith
- The Lundberg Laboratory for Diabetes Research, Department of Molecular and Clinical Medicine, the Sahlgrenska Academy, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Timothy E McGraw
- Department of Biochemistry, Weill Cornell Medical College, New York, NY 10065, USA
| | - Alan Saghatelian
- Clayton Foundation Laboratories for Peptide Biology, Helmsley Center for Genomic Medicine, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA.
| | - Barbara B Kahn
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, 330 Brookline Avenue, Boston, MA 02215, USA.
| |
Collapse
|
43
|
Rathore A, Chu Q, Tan D, Martinez TF, Donaldson CJ, Diedrich JK, Yates JR, Saghatelian A. MIEF1 Microprotein Regulates Mitochondrial Translation. Biochemistry 2018; 57:5564-5575. [PMID: 30215512 DOI: 10.1021/acs.biochem.8b00726] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Recent technological advances led to the discovery of hundreds to thousands of peptides and small proteins (microproteins) encoded by small open reading frames (smORFs). Characterization of new microproteins demonstrates their role in fundamental biological processes and highlights the value in discovering and characterizing more microproteins. The elucidation of microprotein-protein interactions (MPIs) is useful for determining the biochemical and cellular roles of microproteins. In this study, we characterize the protein interaction partners of mitochondrial elongation factor 1 microprotein (MIEF1-MP) using a proximity labeling strategy that relies on APEX2. MIEF1-MP localizes to the mitochondrial matrix where it interacts with the mitochondrial ribosome (mitoribosome). Functional studies demonstrate that MIEF1-MP regulates mitochondrial translation via its binding to the mitoribosome. Loss of MIEF1-MP decreases the mitochondrial translation rate, while an elevated level of MIEF1-MP increases the translation rate. The identification of MIEF1-MP reveals a new gene involved in this process.
Collapse
Affiliation(s)
- Annie Rathore
- Clayton Foundation Laboratories for Peptide Biology , The Salk Institute for Biological Studies , 10010 North Torrey Pines Road , La Jolla , California 92037 , United States.,Division of Biological Sciences , University of California, San Diego , 9500 Gilman Drive , La Jolla , California 92093 , United States
| | - Qian Chu
- Clayton Foundation Laboratories for Peptide Biology , The Salk Institute for Biological Studies , 10010 North Torrey Pines Road , La Jolla , California 92037 , United States
| | - Dan Tan
- Clayton Foundation Laboratories for Peptide Biology , The Salk Institute for Biological Studies , 10010 North Torrey Pines Road , La Jolla , California 92037 , United States
| | - Thomas F Martinez
- Clayton Foundation Laboratories for Peptide Biology , The Salk Institute for Biological Studies , 10010 North Torrey Pines Road , La Jolla , California 92037 , United States
| | - Cynthia J Donaldson
- Clayton Foundation Laboratories for Peptide Biology , The Salk Institute for Biological Studies , 10010 North Torrey Pines Road , La Jolla , California 92037 , United States
| | - Jolene K Diedrich
- Mass Spectrometry Core for Proteomics and Metabolomics , The Salk Institute for Biological Studies , 10010 North Torrey Pines Road , La Jolla , California 92037 , United States.,Department of Molecular Medicine , The Scripps Research Institute , 10550 North Torrey Pines Road , La Jolla , California 92037 , United States
| | - John R Yates
- Department of Molecular Medicine , The Scripps Research Institute , 10550 North Torrey Pines Road , La Jolla , California 92037 , United States
| | - Alan Saghatelian
- Clayton Foundation Laboratories for Peptide Biology , The Salk Institute for Biological Studies , 10010 North Torrey Pines Road , La Jolla , California 92037 , United States
| |
Collapse
|
44
|
Zarrinpar A, Chaix A, Xu ZZ, Chang MW, Marotz CA, Saghatelian A, Knight R, Panda S. Antibiotic-induced microbiome depletion alters metabolic homeostasis by affecting gut signaling and colonic metabolism. Nat Commun 2018; 9:2872. [PMID: 30030441 PMCID: PMC6054678 DOI: 10.1038/s41467-018-05336-9] [Citation(s) in RCA: 296] [Impact Index Per Article: 49.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2017] [Accepted: 06/28/2018] [Indexed: 12/11/2022] Open
Abstract
Antibiotic-induced microbiome depletion (AIMD) has been used frequently to study the role of the gut microbiome in pathological conditions. However, unlike germ-free mice, the effects of AIMD on host metabolism remain incompletely understood. Here we show the effects of AIMD to elucidate its effects on gut homeostasis, luminal signaling, and metabolism. We demonstrate that AIMD, which decreases luminal Firmicutes and Bacteroidetes species, decreases baseline serum glucose levels, reduces glucose surge in a tolerance test, and improves insulin sensitivity without altering adiposity. These changes occur in the setting of decreased luminal short-chain fatty acids (SCFAs), especially butyrate, and the secondary bile acid pool, which affects whole-body bile acid metabolism. In mice, AIMD alters cecal gene expression and gut glucagon-like peptide 1 signaling. Extensive tissue remodeling and decreased availability of SCFAs shift colonocyte metabolism toward glucose utilization. We suggest that AIMD alters glucose homeostasis by potentially shifting colonocyte energy utilization from SCFAs to glucose. Antibiotic-induced microbiome depletion is one of the most common approaches to modulate the gut microbiome. Here the authors demonstrate that it affects gut homeostasis and glucose metabolism by decreasing luminal short chain fatty acids and leading to a shift of energy utilization by colonocytes.
Collapse
Affiliation(s)
- Amir Zarrinpar
- Regulatory Biology Laboratory, The Salk Institute, 10010 N. Torrey Pines Road, La Jolla, CA, 92037, USA. .,Division of Gastroenterology, University of California, San Diego, 9500 Gilman Drive, MC 0983, La Jolla, CA, 92093-0983, USA. .,Center for Microbiome Innovation, University of California, San Diego, 9500 Gilman Drive, MC 0436, La Jolla, CA, 92093-0436, USA. .,Division of Gastroenterology, VA San Diego Health Systems, 3350 La Jolla Village Drive, MC 9111D, La Jolla, CA, 92161, USA.
| | - Amandine Chaix
- Regulatory Biology Laboratory, The Salk Institute, 10010 N. Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Zhenjiang Z Xu
- Center for Microbiome Innovation, University of California, San Diego, 9500 Gilman Drive, MC 0436, La Jolla, CA, 92093-0436, USA.,Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, MC 0763, La Jolla, CA, 92093-0763, USA.,Department of Computer Science and Engineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Max W Chang
- Integrative Genomics and Bioinformatics Core, The Salk Institute, 10010 N. Torrey Pines Road, La Jolla, CA, 92037, USA.,Division of Endocrinology, University of California, San Diego, 9500 Gilman Drive #0640, La Jolla, CA, 92093-0640, USA
| | - Clarisse A Marotz
- Center for Microbiome Innovation, University of California, San Diego, 9500 Gilman Drive, MC 0436, La Jolla, CA, 92093-0436, USA.,Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, MC 0763, La Jolla, CA, 92093-0763, USA
| | - Alan Saghatelian
- Protein Biology Laboratory, The Salk Institute, 10010 N. Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Rob Knight
- Center for Microbiome Innovation, University of California, San Diego, 9500 Gilman Drive, MC 0436, La Jolla, CA, 92093-0436, USA.,Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, MC 0763, La Jolla, CA, 92093-0763, USA.,Department of Computer Science and Engineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Satchidananda Panda
- Regulatory Biology Laboratory, The Salk Institute, 10010 N. Torrey Pines Road, La Jolla, CA, 92037, USA.
| |
Collapse
|
45
|
Mesci P, Macia A, Moore SM, Shiryaev SA, Pinto A, Huang CT, Tejwani L, Fernandes IR, Suarez NA, Kolar MJ, Montefusco S, Rosenberg SC, Herai RH, Cugola FR, Russo FB, Sheets N, Saghatelian A, Shresta S, Momper JD, Siqueira-Neto JL, Corbett KD, Beltrão-Braga PCB, Terskikh AV, Muotri AR. Author Correction: Blocking Zika virus vertical transmission. Sci Rep 2018; 8:8794. [PMID: 29867187 PMCID: PMC5986756 DOI: 10.1038/s41598-018-26959-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has not been fixed in the paper.
Collapse
Affiliation(s)
- Pinar Mesci
- University of California San Diego, School of Medicine, Department of Pediatrics/Rady Children's Hospital San Diego, Department of Cellular & Molecular Medicine, Stem Cell Program, La Jolla, CA, 92037-0695, USA
| | - Angela Macia
- University of California San Diego, School of Medicine, Department of Pediatrics/Rady Children's Hospital San Diego, Department of Cellular & Molecular Medicine, Stem Cell Program, La Jolla, CA, 92037-0695, USA
| | - Spencer M Moore
- University of California San Diego, School of Medicine, Department of Pediatrics/Rady Children's Hospital San Diego, Department of Cellular & Molecular Medicine, Stem Cell Program, La Jolla, CA, 92037-0695, USA
| | - Sergey A Shiryaev
- Sanford Burnham Prebys Medical Discovery Institute, 10901N. Torrey Pines Rd., La Jolla, CA, 92037, USA
| | - Antonella Pinto
- Sanford Burnham Prebys Medical Discovery Institute, 10901N. Torrey Pines Rd., La Jolla, CA, 92037, USA
| | - Chun-Teng Huang
- Sanford Burnham Prebys Medical Discovery Institute, 10901N. Torrey Pines Rd., La Jolla, CA, 92037, USA
| | - Leon Tejwani
- University of California San Diego, School of Medicine, Department of Pediatrics/Rady Children's Hospital San Diego, Department of Cellular & Molecular Medicine, Stem Cell Program, La Jolla, CA, 92037-0695, USA
| | - Isabella R Fernandes
- University of California San Diego, School of Medicine, Department of Pediatrics/Rady Children's Hospital San Diego, Department of Cellular & Molecular Medicine, Stem Cell Program, La Jolla, CA, 92037-0695, USA
| | - Nicole A Suarez
- University of California San Diego, School of Medicine, Department of Pediatrics/Rady Children's Hospital San Diego, Department of Cellular & Molecular Medicine, Stem Cell Program, La Jolla, CA, 92037-0695, USA
| | - Matthew J Kolar
- Salk Institute for Biological Studies, Clayton Foundation Laboratories for Peptide Biology, Helmsley Center for Genomic Medicine, La Jolla, California, USA
| | - Sandro Montefusco
- University of California San Diego, Skaggs School of Pharmacy and Pharmaceutical Sciences, Center for Discovery and Innovation in Parasitic Diseases, 9500 Gilman Dr., La Jolla, CA, 92093, MC 0755, USA
| | - Scott C Rosenberg
- Ludwig Institute for Cancer Research, San Diego Branch, 9500 Gilman Dr., La Jolla, CA, 92093, MC 2385, USA
- University of California San Diego, Department of Cellular and Molecular Medicine, 9500 Gilman Dr., La Jolla, CA, 92093, MC 2385, USA
| | - Roberto H Herai
- Graduate Program in Health Sciences, School of Medicine, Pontifícia Universidade Católica do Paraná (PUCPR), Curitiba, Paraná, Brazil
| | - Fernanda R Cugola
- University of São Paulo, Institute of Biomedical Science, Department of Microbiology, Laboratory of Stem Cell and Disease Modeling, São Paulo, SP, 05508-000, Brazil
- University of São Paulo, School of Arts Sciences and Humanities, Department of Obstetrics, São Paulo, SP, 03828-000, Brazil
- University of São Paulo, School of Medicine, Center for Cellular and Molecular Therapy (NETCEM), São Paulo, SP, 01246-903, Brazil
| | - Fabiele B Russo
- University of São Paulo, Institute of Biomedical Science, Department of Microbiology, Laboratory of Stem Cell and Disease Modeling, São Paulo, SP, 05508-000, Brazil
- University of São Paulo, School of Arts Sciences and Humanities, Department of Obstetrics, São Paulo, SP, 03828-000, Brazil
- University of São Paulo, School of Medicine, Center for Cellular and Molecular Therapy (NETCEM), São Paulo, SP, 01246-903, Brazil
| | - Nicholas Sheets
- Division of Inflammation Biology, La Jolla Institute for Allergy & Immunology, La Jolla, CA, 92037, USA
| | - Alan Saghatelian
- Salk Institute for Biological Studies, Clayton Foundation Laboratories for Peptide Biology, Helmsley Center for Genomic Medicine, La Jolla, California, USA
| | - Sujan Shresta
- Division of Inflammation Biology, La Jolla Institute for Allergy & Immunology, La Jolla, CA, 92037, USA
| | - Jeremiah D Momper
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Jair L Siqueira-Neto
- University of California San Diego, Skaggs School of Pharmacy and Pharmaceutical Sciences, Center for Discovery and Innovation in Parasitic Diseases, 9500 Gilman Dr., La Jolla, CA, 92093, MC 0755, USA
| | - Kevin D Corbett
- Ludwig Institute for Cancer Research, San Diego Branch, 9500 Gilman Dr., La Jolla, CA, 92093, MC 2385, USA
| | - Patricia C B Beltrão-Braga
- University of São Paulo, Institute of Biomedical Science, Department of Microbiology, Laboratory of Stem Cell and Disease Modeling, São Paulo, SP, 05508-000, Brazil.
- University of São Paulo, School of Arts Sciences and Humanities, Department of Obstetrics, São Paulo, SP, 03828-000, Brazil.
- University of São Paulo, School of Medicine, Center for Cellular and Molecular Therapy (NETCEM), São Paulo, SP, 01246-903, Brazil.
| | - Alexey V Terskikh
- Sanford Burnham Prebys Medical Discovery Institute, 10901N. Torrey Pines Rd., La Jolla, CA, 92037, USA.
| | - Alysson R Muotri
- University of California San Diego, School of Medicine, Department of Pediatrics/Rady Children's Hospital San Diego, Department of Cellular & Molecular Medicine, Stem Cell Program, La Jolla, CA, 92037-0695, USA.
| |
Collapse
|
46
|
Chu Q, Rathore A, Diedrich JK, Donaldson CJ, Yates JR, Saghatelian A. Identification of Microprotein‐Protein Interactions via APEX Tagging. FASEB J 2018. [DOI: 10.1096/fasebj.2018.32.1_supplement.530.9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Qian Chu
- The Salk Institute for Biological StudiesLa JollaCA
| | | | | | | | | | | |
Collapse
|
47
|
Kolar MJ, Nelson AT, Chang T, Ertunc ME, Christy MP, Ohlsson L, Härröd M, Kahn BB, Siegel D, Saghatelian A. Faster Protocol for Endogenous Fatty Acid Esters of Hydroxy Fatty Acid (FAHFA) Measurements. Anal Chem 2018; 90:5358-5365. [PMID: 29578702 DOI: 10.1021/acs.analchem.8b00503] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Fatty acid esters of hydroxy fatty acids (FAHFAs) are a recently discovered class of endogenous lipids with antidiabetic and anti-inflammatory activities. Interest in these lipids is due to their unique biological activites and the observation that insulin-resistant people have lower palmitic acid esters of hydroxystearic acid (PAHSA) levels, suggesting that a FAHFA deficiency may contribute to metabolic disease. Rigorous testing of this hypothesis will require the measurement of many clinical samples; however, current analytical workflows are too slow to enable samples to be analyzed quickly. Here we describe the development of a significantly faster workflow to measure FAHFAs that optimizes the fractionation and chromatography of these lipids. We can measure FAHFAs in 30 min with this new protocol versus 90 min using the older protocol with comparable performance in regioisomer detection and quantitation. We also discovered through this optimization that oleic acid esters of hydroxystearic acids (OAHSAs), another family of FAHFAs, have a much lower background signal than PAHSAs, which makes them easier to measure. Our faster workflow was able to quantify changes in PAHSAs and OAHSAs in mouse tissues and human plasma, highlighting the potential of this protocol for basic and clinical applications.
Collapse
Affiliation(s)
- Matthew J Kolar
- Clayton Foundation Laboratories for Peptide Biology , Salk Institute for Biological Studies , 10010 North Torrey Pines Road , La Jolla , California 92037 , United States
| | - Andrew T Nelson
- Skaggs School of Pharmacy and Pharmaceutical Sciences , University of California-San Diego , 9500 Gilman Drive , La Jolla , California 92093 , United States
| | - Tina Chang
- Clayton Foundation Laboratories for Peptide Biology , Salk Institute for Biological Studies , 10010 North Torrey Pines Road , La Jolla , California 92037 , United States
| | - Meric Erikci Ertunc
- Clayton Foundation Laboratories for Peptide Biology , Salk Institute for Biological Studies , 10010 North Torrey Pines Road , La Jolla , California 92037 , United States
| | - Mitchell P Christy
- Skaggs School of Pharmacy and Pharmaceutical Sciences , University of California-San Diego , 9500 Gilman Drive , La Jolla , California 92093 , United States
| | - Lena Ohlsson
- Department of Clinical Sciences, Division of Experimental Vascular Research , Lund University , 221 00 Lund , Sweden
| | - Magnus Härröd
- Härröd Research , Frans Persons väg 6 , 40229 Gothenburg , Sweden
| | - Barbara B Kahn
- Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, Beth Israel Deaconess Medical Center , Harvard Medical School , Boston , Massachusetts 02215 , United States
| | - Dionicio Siegel
- Skaggs School of Pharmacy and Pharmaceutical Sciences , University of California-San Diego , 9500 Gilman Drive , La Jolla , California 92093 , United States
| | - Alan Saghatelian
- Clayton Foundation Laboratories for Peptide Biology , Salk Institute for Biological Studies , 10010 North Torrey Pines Road , La Jolla , California 92037 , United States
| |
Collapse
|
48
|
Muñoz SS, Li H, Ruberu K, Chu Q, Saghatelian A, Ooi L, Garner B. The serine protease HtrA1 contributes to the formation of an extracellular 25-kDa apolipoprotein E fragment that stimulates neuritogenesis. J Biol Chem 2018; 293:4071-4084. [PMID: 29414786 PMCID: PMC5857987 DOI: 10.1074/jbc.ra117.001278] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 01/24/2018] [Indexed: 12/31/2022] Open
Abstract
Apolipoprotein-E (apoE) is a glycoprotein highly expressed in the brain, where it appears to play a role in lipid transport, β-amyloid clearance, and neuronal signaling. ApoE proteolytic fragments are also present in the brain, but the enzymes responsible for apoE fragmentation are unknown, and the biological activity of specific apoE fragments remains to be determined. Here we utilized SK-N-SH neuroblastoma cells differentiated into neurons with all-trans-retinoic acid (ATRA) to study extracellular apoE proteolysis. ApoE fragments were detectable in culture supernatants after 3 days, and their levels were increased for up to 9 days in the presence of ATRA. The concentration of apoE fragments was positively correlated with levels of the neuronal maturation markers (PSD95 and SMI32). The most abundant apoE fragments were 25- and 28-kDa N-terminal fragments that both contained sialylated glycosylation and bound to heparin. We detected apoE fragments only in the extracellular milieu and not in cell lysates, suggesting that an extracellular protease contributes to apoE fragmentation. Of note, siRNA-mediated knockdown of high-temperature requirement serine peptidase A1 (HtrA1) and a specific HtrA1 inhibitor reduced apoE 25-kDa fragment formation by 41 and 86%, respectively. Recombinant 25-kDa fragment apoE and full-length apoE both stimulated neuritogenesis in vitro, increasing neuroblastoma neurite growth by more than 2-fold over a 6-day period. This study provides a cellular model for assessing apoE proteolysis, indicates that HtrA1 regulates apoE 25-kDa fragment formation under physiological conditions, and reveals a new neurotrophic function for the apoE 25-kDa fragment.
Collapse
Affiliation(s)
- Sonia Sanz Muñoz
- From the Illawarra Health and Medical Research Institute and
- the School of Biological Sciences, University of Wollongong, New South Wales 2522, Australia and
| | - Hongyun Li
- From the Illawarra Health and Medical Research Institute and
- the School of Biological Sciences, University of Wollongong, New South Wales 2522, Australia and
| | - Kalani Ruberu
- From the Illawarra Health and Medical Research Institute and
- the School of Biological Sciences, University of Wollongong, New South Wales 2522, Australia and
| | - Qian Chu
- the Clayton Foundation Laboratories for Peptide Biology, Salk Institute for Biological Studies, La Jolla, California 92037
| | - Alan Saghatelian
- the Clayton Foundation Laboratories for Peptide Biology, Salk Institute for Biological Studies, La Jolla, California 92037
| | - Lezanne Ooi
- From the Illawarra Health and Medical Research Institute and
- the School of Biological Sciences, University of Wollongong, New South Wales 2522, Australia and
| | - Brett Garner
- From the Illawarra Health and Medical Research Institute and
- the School of Biological Sciences, University of Wollongong, New South Wales 2522, Australia and
| |
Collapse
|
49
|
Syed I, Lee J, Moraes-Vieira PM, Donaldson CJ, Sontheimer A, Aryal P, Wellenstein K, Kolar MJ, Nelson AT, Siegel D, Mokrosinski J, Farooqi IS, Zhao JJ, Yore MM, Peroni OD, Saghatelian A, Kahn BB. Palmitic Acid Hydroxystearic Acids Activate GPR40, Which Is Involved in Their Beneficial Effects on Glucose Homeostasis. Cell Metab 2018; 27:419-427.e4. [PMID: 29414687 PMCID: PMC5807007 DOI: 10.1016/j.cmet.2018.01.001] [Citation(s) in RCA: 113] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Revised: 08/24/2017] [Accepted: 01/03/2018] [Indexed: 12/28/2022]
Abstract
Palmitic acid hydroxystearic acids (PAHSAs) are endogenous lipids with anti-diabetic and anti-inflammatory effects. PAHSA levels are reduced in serum and adipose tissue of insulin-resistant people and high-fat diet (HFD)-fed mice. Here, we investigated whether chronic PAHSA treatment enhances insulin sensitivity and which receptors mediate PAHSA effects. Chronic PAHSA administration in chow- and HFD-fed mice raises serum and tissue PAHSA levels ∼1.4- to 3-fold. This improves insulin sensitivity and glucose tolerance without altering body weight. PAHSA administration in chow-fed, but not HFD-fed, mice augments insulin and glucagon-like peptide (GLP-1) secretion. PAHSAs are selective agonists for GPR40, increasing Ca+2 flux, but not intracellular cyclic AMP. Blocking GPR40 reverses improvements in glucose tolerance and insulin sensitivity in PAHSA-treated chow- and HFD-fed mice and directly inhibits PAHSA augmentation of glucose-stimulated insulin secretion in human islets. In contrast, GLP-1 receptor blockade in PAHSA-treated chow-fed mice reduces PAHSA effects on glucose tolerance, but not on insulin sensitivity. Thus, PAHSAs activate GPR40, which is involved in their beneficial metabolic effects.
Collapse
Affiliation(s)
- Ismail Syed
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Center for Life Sciences, Room 747, 330 Brookline Avenue, Boston, MA 02215, USA
| | - Jennifer Lee
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Center for Life Sciences, Room 747, 330 Brookline Avenue, Boston, MA 02215, USA
| | - Pedro M Moraes-Vieira
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Center for Life Sciences, Room 747, 330 Brookline Avenue, Boston, MA 02215, USA
| | - Cynthia J Donaldson
- Clayton Foundation Laboratories for Peptide Biology, Helmsley Center for Genomic Medicine, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Alexandra Sontheimer
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Center for Life Sciences, Room 747, 330 Brookline Avenue, Boston, MA 02215, USA
| | - Pratik Aryal
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Center for Life Sciences, Room 747, 330 Brookline Avenue, Boston, MA 02215, USA
| | - Kerry Wellenstein
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Center for Life Sciences, Room 747, 330 Brookline Avenue, Boston, MA 02215, USA
| | - Matthew J Kolar
- Clayton Foundation Laboratories for Peptide Biology, Helmsley Center for Genomic Medicine, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Andrew T Nelson
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Dionicio Siegel
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Jacek Mokrosinski
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Wellcome Trust-MRC Institute of Metabolic Science, Cambridge CB2 0QQ, UK
| | - I Sadaf Farooqi
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Wellcome Trust-MRC Institute of Metabolic Science, Cambridge CB2 0QQ, UK
| | - Juan Juan Zhao
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Center for Life Sciences, Room 747, 330 Brookline Avenue, Boston, MA 02215, USA
| | - Mark M Yore
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Center for Life Sciences, Room 747, 330 Brookline Avenue, Boston, MA 02215, USA
| | - Odile D Peroni
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Center for Life Sciences, Room 747, 330 Brookline Avenue, Boston, MA 02215, USA
| | - Alan Saghatelian
- Clayton Foundation Laboratories for Peptide Biology, Helmsley Center for Genomic Medicine, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Barbara B Kahn
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Center for Life Sciences, Room 747, 330 Brookline Avenue, Boston, MA 02215, USA.
| |
Collapse
|
50
|
Mesci P, Macia A, Moore SM, Shiryaev SA, Pinto A, Huang CT, Tejwani L, Fernandes IR, Suarez NA, Kolar MJ, Montefusco S, Rosenberg SC, Herai RH, Cugola FR, Russo FB, Sheets N, Saghatelian A, Shresta S, Momper JD, Siqueira-Neto JL, Corbett KD, Beltrão-Braga PCB, Terskikh AV, Muotri AR. Blocking Zika virus vertical transmission. Sci Rep 2018; 8:1218. [PMID: 29352135 PMCID: PMC5775359 DOI: 10.1038/s41598-018-19526-4] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 01/04/2018] [Indexed: 12/20/2022] Open
Abstract
The outbreak of the Zika virus (ZIKV) has been associated with increased incidence of congenital malformations. Although recent efforts have focused on vaccine development, treatments for infected individuals are needed urgently. Sofosbuvir (SOF), an FDA-approved nucleotide analog inhibitor of the Hepatitis C (HCV) RNA-dependent RNA polymerase (RdRp) was recently shown to be protective against ZIKV both in vitro and in vivo. Here, we show that SOF protected human neural progenitor cells (NPC) and 3D neurospheres from ZIKV infection-mediated cell death and importantly restored the antiviral immune response in NPCs. In vivo, SOF treatment post-infection (p.i.) decreased viral burden in an immunodeficient mouse model. Finally, we show for the first time that acute SOF treatment of pregnant dams p.i. was well-tolerated and prevented vertical transmission of the virus to the fetus. Taken together, our data confirmed SOF-mediated sparing of human neural cell types from ZIKV-mediated cell death in vitro and reduced viral burden in vivo in animal models of chronic infection and vertical transmission, strengthening the growing body of evidence for SOF anti-ZIKV activity.
Collapse
Affiliation(s)
- Pinar Mesci
- University of California San Diego, School of Medicine, Department of Pediatrics/Rady Children's Hospital San Diego, Department of Cellular & Molecular Medicine, Stem Cell Program, La Jolla, CA, 92037-0695, USA
| | - Angela Macia
- University of California San Diego, School of Medicine, Department of Pediatrics/Rady Children's Hospital San Diego, Department of Cellular & Molecular Medicine, Stem Cell Program, La Jolla, CA, 92037-0695, USA
| | - Spencer M Moore
- University of California San Diego, School of Medicine, Department of Pediatrics/Rady Children's Hospital San Diego, Department of Cellular & Molecular Medicine, Stem Cell Program, La Jolla, CA, 92037-0695, USA
| | - Sergey A Shiryaev
- Sanford Burnham Prebys Medical Discovery Institute, 10901N. Torrey Pines Rd., La Jolla, CA, 92037, USA
| | - Antonella Pinto
- Sanford Burnham Prebys Medical Discovery Institute, 10901N. Torrey Pines Rd., La Jolla, CA, 92037, USA
| | - Chun-Teng Huang
- Sanford Burnham Prebys Medical Discovery Institute, 10901N. Torrey Pines Rd., La Jolla, CA, 92037, USA
| | - Leon Tejwani
- University of California San Diego, School of Medicine, Department of Pediatrics/Rady Children's Hospital San Diego, Department of Cellular & Molecular Medicine, Stem Cell Program, La Jolla, CA, 92037-0695, USA
| | - Isabella R Fernandes
- University of California San Diego, School of Medicine, Department of Pediatrics/Rady Children's Hospital San Diego, Department of Cellular & Molecular Medicine, Stem Cell Program, La Jolla, CA, 92037-0695, USA
| | - Nicole A Suarez
- University of California San Diego, School of Medicine, Department of Pediatrics/Rady Children's Hospital San Diego, Department of Cellular & Molecular Medicine, Stem Cell Program, La Jolla, CA, 92037-0695, USA
| | - Matthew J Kolar
- Salk Institute for Biological Studies, Clayton Foundation Laboratories for Peptide Biology, Helmsley Center for Genomic Medicine, La Jolla, California, USA
| | - Sandro Montefusco
- University of California San Diego, Skaggs School of Pharmacy and Pharmaceutical Sciences, Center for Discovery and Innovation in Parasitic Diseases, 9500 Gilman Dr., La Jolla, CA, 92093, MC 0755, USA
| | - Scott C Rosenberg
- Ludwig Institute for Cancer Research, San Diego Branch, 9500 Gilman Dr., La Jolla, CA, 92093, MC 2385, USA
- University of California San Diego, Department of Cellular and Molecular Medicine, 9500 Gilman Dr., La Jolla, CA, 92093, MC 2385, USA
| | - Roberto H Herai
- Graduate Program in Health Sciences, School of Medicine, Pontifícia Universidade Católica do Paraná (PUCPR), Curitiba, Paraná, Brazil
| | - Fernanda R Cugola
- University of São Paulo, Institute of Biomedical Science, Department of Microbiology, Laboratory of Stem Cell and Disease Modeling, São Paulo, SP, 05508-000, Brazil
- University of São Paulo, School of Arts Sciences and Humanities, Department of Obstetrics, São Paulo, SP, 03828-000, Brazil
- University of São Paulo, School of Medicine, Center for Cellular and Molecular Therapy (NETCEM), São Paulo, SP, 01246-903, Brazil
| | - Fabiele B Russo
- University of São Paulo, Institute of Biomedical Science, Department of Microbiology, Laboratory of Stem Cell and Disease Modeling, São Paulo, SP, 05508-000, Brazil
- University of São Paulo, School of Arts Sciences and Humanities, Department of Obstetrics, São Paulo, SP, 03828-000, Brazil
- University of São Paulo, School of Medicine, Center for Cellular and Molecular Therapy (NETCEM), São Paulo, SP, 01246-903, Brazil
| | - Nicholas Sheets
- Division of Inflammation Biology, La Jolla Institute for Allergy & Immunology, La Jolla, CA, 92037, USA
| | - Alan Saghatelian
- Salk Institute for Biological Studies, Clayton Foundation Laboratories for Peptide Biology, Helmsley Center for Genomic Medicine, La Jolla, California, USA
| | - Sujan Shresta
- Division of Inflammation Biology, La Jolla Institute for Allergy & Immunology, La Jolla, CA, 92037, USA
| | - Jeremiah D Momper
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Jair L Siqueira-Neto
- University of California San Diego, Skaggs School of Pharmacy and Pharmaceutical Sciences, Center for Discovery and Innovation in Parasitic Diseases, 9500 Gilman Dr., La Jolla, CA, 92093, MC 0755, USA
| | - Kevin D Corbett
- Ludwig Institute for Cancer Research, San Diego Branch, 9500 Gilman Dr., La Jolla, CA, 92093, MC 2385, USA
| | - Patricia C B Beltrão-Braga
- University of São Paulo, Institute of Biomedical Science, Department of Microbiology, Laboratory of Stem Cell and Disease Modeling, São Paulo, SP, 05508-000, Brazil.
- University of São Paulo, School of Arts Sciences and Humanities, Department of Obstetrics, São Paulo, SP, 03828-000, Brazil.
- University of São Paulo, School of Medicine, Center for Cellular and Molecular Therapy (NETCEM), São Paulo, SP, 01246-903, Brazil.
| | - Alexey V Terskikh
- Sanford Burnham Prebys Medical Discovery Institute, 10901N. Torrey Pines Rd., La Jolla, CA, 92037, USA.
| | - Alysson R Muotri
- University of California San Diego, School of Medicine, Department of Pediatrics/Rady Children's Hospital San Diego, Department of Cellular & Molecular Medicine, Stem Cell Program, La Jolla, CA, 92037-0695, USA.
| |
Collapse
|